GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in STES-TP
Stomach and Esophageal carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C15D8R9X
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in STES-TP. Broad Institute of MIT and Harvard. doi:10.7908/C15D8R9X
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "STES-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

  1. For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.

  2. Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).

  3. Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).

  4. Checks if the top core genes are up-regulated or down-regulated.

  5. Checks if the top core genes are high expressed or low expressed.

  6. Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 726
Number of samples: 599
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 170
pheno.type: 2 - 3 :[ clus2 ] 275
pheno.type: 3 - 3 :[ clus3 ] 154

For the expression subtypes of 18744 genes in 600 samples, GSEA found enriched gene sets in each cluster using 599 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are PID P73PATHWAY, PID MTOR 4PATHWAY, PID MYC PATHWAY, PID DELTANP63PATHWAY, PID AURORA A PATHWAY, PID TAP63PATHWAY, PID P53REGULATIONPATHWAY, REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, REACTOME MEMBRANE TRAFFICKING, REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

    • And common core enriched genes are YWHAE, YWHAG, SFN, ALMS1, AZI1, CCNB1, CDK1, CDK5RAP2, CEP164, CEP250

  • clus2

    • Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG SPHINGOLIPID METABOLISM, KEGG PYRUVATE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG BASE EXCISION REPAIR, KEGG PEROXISOME

    • And common core enriched genes are ALDOB, FBP1, FBP2, AARS2, CARS2, DARS2, EARS2, EPRS, FARSB, HARS2

  • clus3

    • Top enriched gene sets are KEGG PURINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG ABC TRANSPORTERS, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY

    • And common core enriched genes are PIK3R1, AKT3, RPS6KA2, MEF2C, PRKCB, CAB39L, FIGF, IGF1, PIK3CD, PIK3CG

Results
Subtype clus1 enriched pathways

Table 3.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
PID P73PATHWAY 79 genes.ES.table 0.46 1.8 0.012 0.35 0.65 0.15 0.095 0.14 0.096 0.089
PID MTOR 4PATHWAY 67 genes.ES.table 0.44 2.1 0.0041 0.21 0.1 0.54 0.34 0.36 0 0.057
PID MYC PATHWAY 25 genes.ES.table 0.43 1.6 0.03 0.48 0.91 0.6 0.35 0.39 0.23 0.13
PID DELTANP63PATHWAY 47 genes.ES.table 0.67 2 0 0.22 0.27 0.45 0.18 0.37 0 0.045
PID AURORA A PATHWAY 31 genes.ES.table 0.53 1.8 0.032 0.36 0.63 0.48 0.27 0.36 0.095 0.09
PID TAP63PATHWAY 54 genes.ES.table 0.49 1.7 0.0098 0.47 0.88 0.2 0.096 0.18 0.2 0.13
PID P53REGULATIONPATHWAY 58 genes.ES.table 0.35 1.6 0.062 0.51 0.91 0.31 0.28 0.22 0.24 0.14
REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 38 genes.ES.table 0.49 1.8 0.0061 0.3 0.54 0.1 0.041 0.1 0.072 0.076
REACTOME MEMBRANE TRAFFICKING 124 genes.ES.table 0.36 2 0 0.21 0.2 0.081 0.038 0.078 0 0.046
REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 65 genes.ES.table 0.4 1.6 0.061 0.52 0.91 0.63 0.37 0.4 0.24 0.14
genes ES table in pathway: PID P73PATHWAY

Table S1.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SFN SFN SFN 320 0.56 0.078 YES
2 BNIP3 BNIP3 BNIP3 500 0.46 0.15 YES
3 SGK1 SGK1 SGK1 1285 0.25 0.15 YES
4 HRAS HRAS HRAS 1461 0.23 0.18 YES
5 ULK2 ULK2 ULK2 1697 0.2 0.2 YES
6 PLD2 PLD2 PLD2 1701 0.2 0.23 YES
7 ULK1 ULK1 ULK1 1706 0.2 0.27 YES
8 RRAGD RRAGD RRAGD 1752 0.2 0.3 YES
9 PLD1 PLD1 PLD1 1801 0.19 0.33 YES
10 CLIP1 CLIP1 CLIP1 2131 0.17 0.34 YES
11 EIF4EBP1 EIF4EBP1 EIF4EBP1 2419 0.15 0.35 YES
12 SREBF1 SREBF1 SREBF1 2970 0.12 0.34 YES
13 YWHAQ YWHAQ YWHAQ 3107 0.11 0.35 YES
14 RRAGC RRAGC RRAGC 3218 0.11 0.37 YES
15 RB1CC1 RB1CC1 RB1CC1 3385 0.1 0.38 YES
16 DDIT4 DDIT4 DDIT4 3476 0.1 0.39 YES
17 BRAF BRAF BRAF 3838 0.089 0.38 YES
18 CCNE1 CCNE1 CCNE1 3935 0.086 0.39 YES
19 YWHAG YWHAG YWHAG 4068 0.082 0.4 YES
20 MAP2K1 MAP2K1 MAP2K1 4101 0.081 0.41 YES
21 RICTOR RICTOR RICTOR 4192 0.079 0.42 YES
22 YWHAZ YWHAZ YWHAZ 4310 0.076 0.43 YES
23 RPS6KB1 RPS6KB1 RPS6KB1 4351 0.074 0.44 YES
24 PML PML PML 4580 0.07 0.44 YES
25 IRS1 IRS1 IRS1 5183 0.057 0.42 YES
26 YY1 YY1 YY1 5218 0.056 0.42 YES
27 YWHAE YWHAE YWHAE 5219 0.056 0.43 YES
28 NRAS NRAS NRAS 5558 0.05 0.42 YES
29 MAPK1 MAPK1 MAPK1 5571 0.05 0.43 YES
30 EIF4A1 EIF4A1 EIF4A1 5590 0.05 0.44 YES
31 POLDIP3 POLDIP3 POLDIP3 5660 0.048 0.44 YES
32 RPTOR RPTOR RPTOR 5913 0.044 0.44 YES
33 EIF4E EIF4E EIF4E 5968 0.043 0.44 YES
34 MTOR MTOR MTOR 6160 0.04 0.44 YES
35 TSC1 TSC1 TSC1 6253 0.038 0.44 YES
36 IKBKB IKBKB IKBKB 6285 0.038 0.44 YES
37 PDCD4 PDCD4 PDCD4 6579 0.033 0.44 NO
38 PXN PXN PXN 6796 0.03 0.43 NO
39 CDK2 CDK2 CDK2 6985 0.027 0.42 NO
40 RAF1 RAF1 RAF1 7089 0.026 0.42 NO
41 RHEB RHEB RHEB 7143 0.025 0.42 NO
42 TSC2 TSC2 TSC2 7359 0.022 0.42 NO
43 RAC1 RAC1 RAC1 7739 0.017 0.4 NO
44 RRAGA RRAGA RRAGA 7890 0.015 0.39 NO
45 RRN3 RRN3 RRN3 7997 0.014 0.39 NO
46 MAP2K2 MAP2K2 MAP2K2 8119 0.012 0.38 NO
47 MAPKAP1 MAPKAP1 MAPKAP1 8177 0.011 0.38 NO
48 EEF2K EEF2K EEF2K 8498 0.0061 0.37 NO
49 AKT1 AKT1 AKT1 8502 0.0061 0.37 NO
50 RRAGB RRAGB RRAGB 8960 -0.0002 0.34 NO
51 FBXW11 FBXW11 FBXW11 9148 -0.0028 0.33 NO
52 KRAS KRAS KRAS 9364 -0.0063 0.32 NO
53 AKT1S1 AKT1S1 AKT1S1 9827 -0.013 0.3 NO
54 PRR5 PRR5 PRR5 10016 -0.015 0.29 NO
55 EEF2 EEF2 EEF2 10370 -0.021 0.28 NO
56 YWHAB YWHAB YWHAB 10495 -0.023 0.28 NO
57 MLST8 MLST8 MLST8 10744 -0.027 0.27 NO
58 CYCS CYCS CYCS 11050 -0.033 0.26 NO
59 EIF4B EIF4B EIF4B 11247 -0.036 0.25 NO
60 PDPK1 PDPK1 PDPK1 11777 -0.046 0.23 NO
61 RHOA RHOA RHOA 12463 -0.06 0.2 NO
62 YWHAH YWHAH YWHAH 12704 -0.066 0.2 NO
63 RPS6KA1 RPS6KA1 RPS6KA1 13008 -0.073 0.2 NO
64 SSPO SSPO SSPO 13687 -0.092 0.18 NO
65 MAPK3 MAPK3 MAPK3 14407 -0.12 0.16 NO
66 PPARGC1A PPARGC1A PPARGC1A 15612 -0.18 0.13 NO
67 PRKCA PRKCA PRKCA 16373 -0.23 0.13 NO

Figure S1.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P73PATHWAY.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: PID P73PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID MTOR 4PATHWAY

Table S2.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NINL NINL NINL 1200 0.26 0.0025 YES
2 TUBA4A TUBA4A TUBA4A 1878 0.18 0.013 YES
3 PLK4 PLK4 PLK4 2039 0.17 0.048 YES
4 TUBG2 TUBG2 TUBG2 2147 0.16 0.084 YES
5 TUBGCP5 TUBGCP5 TUBGCP5 2423 0.15 0.11 YES
6 CLASP1 CLASP1 CLASP1 2662 0.13 0.13 YES
7 NEDD1 NEDD1 NEDD1 3045 0.12 0.14 YES
8 CDK1 CDK1 CDK1 3060 0.12 0.16 YES
9 CCNB1 CCNB1 CCNB1 3491 0.1 0.17 YES
10 NEK2 NEK2 NEK2 3636 0.095 0.18 YES
11 CEP250 CEP250 CEP250 3782 0.091 0.2 YES
12 YWHAG YWHAG YWHAG 4068 0.082 0.2 YES
13 TUBG1 TUBG1 TUBG1 4174 0.08 0.22 YES
14 CEP164 CEP164 CEP164 4267 0.077 0.23 YES
15 CSNK1E CSNK1E CSNK1E 4282 0.076 0.25 YES
16 CEP70 CEP70 CEP70 4337 0.075 0.27 YES
17 DYNC1H1 DYNC1H1 DYNC1H1 4369 0.074 0.29 YES
18 CDK5RAP2 CDK5RAP2 CDK5RAP2 4376 0.074 0.3 YES
19 CKAP5 CKAP5 CKAP5 4411 0.073 0.32 YES
20 ALMS1 ALMS1 ALMS1 4429 0.073 0.34 YES
21 CETN2 CETN2 CETN2 4433 0.073 0.36 YES
22 DCTN1 DCTN1 DCTN1 4647 0.068 0.36 YES
23 CEP76 CEP76 CEP76 4689 0.068 0.38 YES
24 PCNT PCNT PCNT 4725 0.067 0.39 YES
25 AZI1 AZI1 AZI1 4807 0.065 0.4 YES
26 PLK1 PLK1 PLK1 4956 0.062 0.41 YES
27 TUBB TUBB TUBB 4981 0.061 0.43 YES
28 HAUS2 HAUS2 HAUS2 5022 0.06 0.44 YES
29 NUMA1 NUMA1 NUMA1 5057 0.06 0.45 YES
30 PAFAH1B1 PAFAH1B1 PAFAH1B1 5068 0.059 0.47 YES
31 YWHAE YWHAE YWHAE 5219 0.056 0.47 YES
32 CEP72 CEP72 CEP72 5224 0.056 0.49 YES
33 CEP63 CEP63 CEP63 5345 0.054 0.5 YES
34 TUBGCP6 TUBGCP6 TUBGCP6 5473 0.052 0.5 YES
35 DYNLL1 DYNLL1 DYNLL1 5698 0.048 0.5 YES
36 SDCCAG8 SDCCAG8 SDCCAG8 5966 0.043 0.5 NO
37 CEP135 CEP135 CEP135 6201 0.039 0.5 NO
38 CENPJ CENPJ CENPJ 6424 0.036 0.49 NO
39 HSP90AA1 HSP90AA1 HSP90AA1 6490 0.035 0.5 NO
40 CEP192 CEP192 CEP192 6757 0.031 0.49 NO
41 DCTN2 DCTN2 DCTN2 6936 0.028 0.49 NO
42 DYNC1I2 DYNC1I2 DYNC1I2 7206 0.024 0.48 NO
43 CEP290 CEP290 CEP290 7371 0.022 0.48 NO
44 DCTN3 DCTN3 DCTN3 7513 0.02 0.48 NO
45 AKAP9 AKAP9 AKAP9 7765 0.016 0.47 NO
46 SSNA1 SSNA1 SSNA1 7859 0.015 0.46 NO
47 ACTR1A ACTR1A ACTR1A 8080 0.012 0.46 NO
48 TUBGCP3 TUBGCP3 TUBGCP3 8110 0.012 0.46 NO
49 MAPRE1 MAPRE1 MAPRE1 8582 0.0052 0.43 NO
50 TUBGCP2 TUBGCP2 TUBGCP2 8687 0.0038 0.43 NO
51 PRKACA PRKACA PRKACA 9387 -0.0067 0.39 NO
52 PPP2R1A PPP2R1A PPP2R1A 9593 -0.0095 0.38 NO
53 CSNK1D CSNK1D CSNK1D 9676 -0.011 0.38 NO
54 OFD1 OFD1 OFD1 10597 -0.024 0.34 NO
55 TUBA1A TUBA1A TUBA1A 10787 -0.028 0.34 NO
56 PCM1 PCM1 PCM1 11192 -0.036 0.32 NO
57 CEP57 CEP57 CEP57 11556 -0.042 0.32 NO
58 FGFR1OP FGFR1OP FGFR1OP 13193 -0.078 0.25 NO
59 PRKAR2B PRKAR2B PRKAR2B 15801 -0.19 0.16 NO

Figure S3.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MTOR 4PATHWAY.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID MYC PATHWAY

Table S3.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GJB6 GJB6 GJB6 27 1 0.076 YES
2 GJB5 GJB5 GJB5 169 0.72 0.12 YES
3 TPD52L1 TPD52L1 TPD52L1 318 0.56 0.16 YES
4 GJB2 GJB2 GJB2 368 0.53 0.19 YES
5 GJA3 GJA3 GJA3 393 0.51 0.23 YES
6 GJB3 GJB3 GJB3 502 0.46 0.26 YES
7 CLTCL1 CLTCL1 CLTCL1 531 0.44 0.29 YES
8 GJB7 GJB7 GJB7 675 0.39 0.31 YES
9 GJA1 GJA1 GJA1 709 0.38 0.34 YES
10 GJB4 GJB4 GJB4 719 0.37 0.36 YES
11 DNM1 DNM1 DNM1 1802 0.19 0.32 NO
12 AP4E1 AP4E1 AP4E1 2346 0.15 0.3 NO
13 TFRC TFRC TFRC 3383 0.1 0.25 NO
14 AP2M1 AP2M1 AP2M1 3652 0.094 0.25 NO
15 HGS HGS HGS 3769 0.092 0.25 NO
16 GJA9 GJA9 GJA9 4122 0.081 0.24 NO
17 VPS4B VPS4B VPS4B 4745 0.066 0.21 NO
18 TJP1 TJP1 TJP1 5056 0.06 0.19 NO
19 VPS37D VPS37D VPS37D 5170 0.057 0.19 NO
20 AP1M1 AP1M1 AP1M1 5470 0.052 0.18 NO
21 IGF2R IGF2R IGF2R 5519 0.051 0.18 NO
22 STAM STAM STAM 5773 0.046 0.17 NO
23 SEC24B SEC24B SEC24B 5978 0.043 0.16 NO
24 AP1G1 AP1G1 AP1G1 6222 0.039 0.15 NO
25 VTA1 VTA1 VTA1 6252 0.038 0.15 NO
26 AP1B1 AP1B1 AP1B1 6320 0.037 0.15 NO
27 COPB2 COPB2 COPB2 6480 0.035 0.15 NO
28 SEC24C SEC24C SEC24C 6608 0.033 0.14 NO
29 CLTC CLTC CLTC 6774 0.03 0.14 NO
30 GBF1 GBF1 GBF1 6850 0.029 0.13 NO
31 AP3S1 AP3S1 AP3S1 6884 0.029 0.14 NO
32 CLTB CLTB CLTB 7054 0.026 0.13 NO
33 PLDN PLDN PLDN 7080 0.026 0.13 NO
34 SNAPIN SNAPIN SNAPIN 7627 0.018 0.1 NO
35 CHMP5 CHMP5 CHMP5 7654 0.018 0.1 NO
36 M6PR M6PR M6PR 7730 0.017 0.098 NO
37 PUM1 PUM1 PUM1 7818 0.016 0.094 NO
38 VPS37C VPS37C VPS37C 7916 0.015 0.09 NO
39 OCRL OCRL OCRL 8029 0.013 0.085 NO
40 AP3B1 AP3B1 AP3B1 8114 0.012 0.081 NO
41 PICALM PICALM PICALM 8172 0.011 0.079 NO
42 VPS4A VPS4A VPS4A 8238 0.01 0.076 NO
43 VAMP8 VAMP8 VAMP8 8276 0.0095 0.075 NO
44 GJD2 GJD2 GJD2 8481 0.0063 0.064 NO
45 VPS25 VPS25 VPS25 8497 0.0061 0.064 NO
46 VAMP7 VAMP7 VAMP7 8527 0.0058 0.063 NO
47 SEC31A SEC31A SEC31A 8711 0.0036 0.053 NO
48 VPS37A VPS37A VPS37A 8867 0.0012 0.045 NO
49 DNAJC6 DNAJC6 DNAJC6 8956 -0.00017 0.04 NO
50 SH3GL2 SH3GL2 SH3GL2 9062 -0.0017 0.035 NO
51 FTH1 FTH1 FTH1 9288 -0.0051 0.023 NO
52 COPG COPG COPG 9295 -0.0052 0.023 NO
53 COPB1 COPB1 COPB1 9337 -0.0059 0.022 NO
54 SNF8 SNF8 SNF8 9585 -0.0094 0.0089 NO
55 SEC23A SEC23A SEC23A 9606 -0.0097 0.0086 NO
56 YIPF6 YIPF6 YIPF6 9690 -0.011 0.0049 NO
57 GJC1 GJC1 GJC1 9734 -0.011 0.0034 NO
58 TSG101 TSG101 TSG101 9778 -0.012 0.002 NO
59 BLOC1S3 BLOC1S3 BLOC1S3 10074 -0.016 -0.013 NO
60 RPS27A RPS27A RPS27A 10338 -0.02 -0.025 NO
61 CLTA CLTA CLTA 10356 -0.021 -0.025 NO
62 NAPA NAPA NAPA 10369 -0.021 -0.024 NO
63 COPE COPE COPE 10372 -0.021 -0.022 NO
64 GJD4 GJD4 GJD4 10745 -0.027 -0.04 NO
65 HSPA8 HSPA8 HSPA8 10783 -0.028 -0.04 NO
66 ARF1 ARF1 ARF1 10803 -0.028 -0.039 NO
67 CHMP6 CHMP6 CHMP6 10806 -0.028 -0.037 NO
68 UBA52 UBA52 UBA52 10872 -0.029 -0.038 NO
69 COPA COPA COPA 10989 -0.032 -0.042 NO
70 HIP1R HIP1R HIP1R 11136 -0.034 -0.048 NO
71 VPS36 VPS36 VPS36 11205 -0.036 -0.049 NO
72 VPS28 VPS28 VPS28 11258 -0.037 -0.049 NO
73 CHMP4A CHMP4A CHMP4A 11268 -0.037 -0.046 NO
74 CNO CNO CNO 11432 -0.04 -0.052 NO
75 ARFGAP1 ARFGAP1 ARFGAP1 11567 -0.042 -0.056 NO
76 DNASE2 DNASE2 DNASE2 11570 -0.042 -0.053 NO
77 PREB PREB PREB 11586 -0.042 -0.051 NO
78 VPS37B VPS37B VPS37B 11610 -0.043 -0.049 NO
79 COPZ1 COPZ1 COPZ1 11622 -0.043 -0.046 NO
80 STAM2 STAM2 STAM2 11662 -0.044 -0.045 NO
81 NECAP1 NECAP1 NECAP1 11706 -0.045 -0.044 NO
82 SNX5 SNX5 SNX5 11753 -0.046 -0.043 NO
83 VAMP2 VAMP2 VAMP2 11994 -0.05 -0.052 NO
84 ARCN1 ARCN1 ARCN1 12051 -0.052 -0.052 NO
85 GAK GAK GAK 12247 -0.056 -0.058 NO
86 SORT1 SORT1 SORT1 12257 -0.056 -0.054 NO
87 DNM2 DNM2 DNM2 12309 -0.057 -0.053 NO
88 AP1S2 AP1S2 AP1S2 12409 -0.059 -0.054 NO
89 SNX2 SNX2 SNX2 12527 -0.062 -0.055 NO
90 STX4 STX4 STX4 12628 -0.064 -0.056 NO
91 PIK3C2A PIK3C2A PIK3C2A 12638 -0.064 -0.052 NO
92 RAB5C RAB5C RAB5C 12730 -0.066 -0.051 NO
93 SH3D19 SH3D19 SH3D19 12862 -0.069 -0.053 NO
94 AP1M2 AP1M2 AP1M2 12957 -0.072 -0.053 NO
95 CPD CPD CPD 12992 -0.072 -0.05 NO
96 CHMP2A CHMP2A CHMP2A 13199 -0.078 -0.055 NO
97 SRC SRC SRC 13256 -0.079 -0.052 NO
98 GNS GNS GNS 13312 -0.081 -0.049 NO
99 TXNDC5 TXNDC5 TXNDC5 13369 -0.082 -0.046 NO
100 SAR1B SAR1B SAR1B 13375 -0.082 -0.04 NO
101 SNAP23 SNAP23 SNAP23 13388 -0.083 -0.034 NO
102 SEC13 SEC13 SEC13 13576 -0.088 -0.038 NO
103 SNX9 SNX9 SNX9 13695 -0.092 -0.037 NO
104 AP1S1 AP1S1 AP1S1 13722 -0.093 -0.032 NO
105 FTL FTL FTL 13768 -0.094 -0.027 NO
106 TGOLN2 TGOLN2 TGOLN2 13873 -0.098 -0.026 NO
107 CHMP7 CHMP7 CHMP7 13897 -0.099 -0.019 NO
108 CHMP4B CHMP4B CHMP4B 14006 -0.1 -0.018 NO
109 MYO6 MYO6 MYO6 14086 -0.1 -0.014 NO
110 AP4B1 AP4B1 AP4B1 14459 -0.12 -0.025 NO
111 CHMP2B CHMP2B CHMP2B 14657 -0.13 -0.026 NO
112 BLOC1S1 BLOC1S1 BLOC1S1 14672 -0.13 -0.017 NO
113 TPD52 TPD52 TPD52 14712 -0.13 -0.0096 NO
114 SEC24D SEC24D SEC24D 14853 -0.14 -0.0069 NO
115 TBC1D8B TBC1D8B TBC1D8B 15012 -0.14 -0.0046 NO
116 CTSZ CTSZ CTSZ 15195 -0.15 -0.003 NO
117 CHMP4C CHMP4C CHMP4C 15266 -0.16 0.0051 NO
118 DTNBP1 DTNBP1 DTNBP1 15426 -0.17 0.009 NO
119 DAB2 DAB2 DAB2 16081 -0.21 -0.01 NO
120 GJC2 GJC2 GJC2 16193 -0.22 -0.00018 NO
121 GJA5 GJA5 GJA5 16709 -0.26 -0.0087 NO
122 GJA4 GJA4 GJA4 17284 -0.31 -0.016 NO
123 ARRB1 ARRB1 ARRB1 18370 -0.51 -0.036 NO
124 GJB1 GJB1 GJB1 18670 -0.74 0.0029 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MYC PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: PID MYC PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID DELTANP63PATHWAY

Table S4.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 KRT5 KRT5 KRT5 3 1.2 0.12 YES
2 KRT14 KRT14 KRT14 12 1.2 0.23 YES
3 TP63 TP63 TP63 14 1.1 0.34 YES
4 DLX5 DLX5 DLX5 120 0.81 0.41 YES
5 RAB38 RAB38 RAB38 141 0.76 0.48 YES
6 IL1A IL1A IL1A 227 0.64 0.54 YES
7 SFN SFN SFN 320 0.56 0.59 YES
8 PERP PERP PERP 617 0.41 0.61 YES
9 NRG1 NRG1 NRG1 802 0.35 0.63 YES
10 DLX6 DLX6 DLX6 910 0.32 0.66 YES
11 TCF7L1 TCF7L1 TCF7L1 1400 0.24 0.66 YES
12 ADA ADA ADA 1772 0.2 0.66 YES
13 SEC14L2 SEC14L2 SEC14L2 2325 0.15 0.64 YES
14 ITGA3 ITGA3 ITGA3 2806 0.13 0.63 YES
15 RRAD RRAD RRAD 2821 0.13 0.64 YES
16 CCNB2 CCNB2 CCNB2 2959 0.12 0.64 YES
17 FASN FASN FASN 3131 0.11 0.64 YES
18 BDKRB2 BDKRB2 BDKRB2 3177 0.11 0.65 YES
19 HELLS HELLS HELLS 3225 0.11 0.66 YES
20 TOP2A TOP2A TOP2A 3226 0.11 0.67 YES
21 NOTCH1 NOTCH1 NOTCH1 3378 0.1 0.67 YES
22 BRCA2 BRCA2 BRCA2 4050 0.083 0.64 NO
23 GSK3B GSK3B GSK3B 4133 0.08 0.65 NO
24 T T T 4301 0.076 0.65 NO
25 HBP1 HBP1 HBP1 4840 0.064 0.62 NO
26 YAP1 YAP1 YAP1 4955 0.062 0.62 NO
27 RUNX1 RUNX1 RUNX1 5117 0.058 0.62 NO
28 FOSL2 FOSL2 FOSL2 5643 0.049 0.6 NO
29 MRE11A MRE11A MRE11A 6354 0.037 0.56 NO
30 ITCH ITCH ITCH 6412 0.036 0.56 NO
31 FBXW7 FBXW7 FBXW7 6452 0.035 0.56 NO
32 HES1 HES1 HES1 6477 0.035 0.57 NO
33 CEBPD CEBPD CEBPD 7284 0.023 0.53 NO
34 STXBP4 STXBP4 STXBP4 7442 0.021 0.52 NO
35 ADRM1 ADRM1 ADRM1 7781 0.016 0.5 NO
36 MDM2 MDM2 MDM2 7999 0.014 0.49 NO
37 PPP2R5A PPP2R5A PPP2R5A 8308 0.0089 0.48 NO
38 COL5A1 COL5A1 COL5A1 9927 -0.014 0.39 NO
39 GNB2L1 GNB2L1 GNB2L1 11108 -0.034 0.33 NO
40 IGFBP3 IGFBP3 IGFBP3 11298 -0.037 0.32 NO
41 VDR VDR VDR 11500 -0.041 0.32 NO
42 ATM ATM ATM 11697 -0.045 0.31 NO
43 WWP1 WWP1 WWP1 12231 -0.056 0.29 NO
44 AXL AXL AXL 13205 -0.078 0.24 NO
45 CDKN2A CDKN2A CDKN2A 13490 -0.086 0.24 NO
46 POU2F2 POU2F2 POU2F2 16203 -0.22 0.11 NO
47 GPX2 GPX2 GPX2 16251 -0.22 0.13 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID DELTANP63PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: PID DELTANP63PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID AURORA A PATHWAY

Table S5.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCNA1 CCNA1 CCNA1 187 0.7 0.11 YES
2 NINL NINL NINL 1200 0.26 0.1 YES
3 TUBA4A TUBA4A TUBA4A 1878 0.18 0.1 YES
4 PLK4 PLK4 PLK4 2039 0.17 0.12 YES
5 PKMYT1 PKMYT1 PKMYT1 2133 0.17 0.14 YES
6 TUBG2 TUBG2 TUBG2 2147 0.16 0.17 YES
7 MNAT1 MNAT1 MNAT1 2390 0.15 0.19 YES
8 TUBGCP5 TUBGCP5 TUBGCP5 2423 0.15 0.21 YES
9 CLASP1 CLASP1 CLASP1 2662 0.13 0.22 YES
10 CCNB2 CCNB2 CCNB2 2959 0.12 0.23 YES
11 NEDD1 NEDD1 NEDD1 3045 0.12 0.24 YES
12 CDK1 CDK1 CDK1 3060 0.12 0.26 YES
13 WEE1 WEE1 WEE1 3127 0.11 0.28 YES
14 CCNB1 CCNB1 CCNB1 3491 0.1 0.28 YES
15 CCNA2 CCNA2 CCNA2 3617 0.096 0.29 YES
16 NEK2 NEK2 NEK2 3636 0.095 0.3 YES
17 CEP250 CEP250 CEP250 3782 0.091 0.31 YES
18 YWHAG YWHAG YWHAG 4068 0.082 0.31 YES
19 TUBG1 TUBG1 TUBG1 4174 0.08 0.32 YES
20 CEP164 CEP164 CEP164 4267 0.077 0.32 YES
21 CSNK1E CSNK1E CSNK1E 4282 0.076 0.34 YES
22 CEP70 CEP70 CEP70 4337 0.075 0.35 YES
23 DYNC1H1 DYNC1H1 DYNC1H1 4369 0.074 0.36 YES
24 CDK5RAP2 CDK5RAP2 CDK5RAP2 4376 0.074 0.37 YES
25 XPO1 XPO1 XPO1 4378 0.074 0.38 YES
26 CKAP5 CKAP5 CKAP5 4411 0.073 0.4 YES
27 ALMS1 ALMS1 ALMS1 4429 0.073 0.41 YES
28 CETN2 CETN2 CETN2 4433 0.073 0.42 YES
29 DCTN1 DCTN1 DCTN1 4647 0.068 0.42 YES
30 CEP76 CEP76 CEP76 4689 0.068 0.43 YES
31 PCNT PCNT PCNT 4725 0.067 0.44 YES
32 AZI1 AZI1 AZI1 4807 0.065 0.45 YES
33 PLK1 PLK1 PLK1 4956 0.062 0.45 YES
34 TUBB TUBB TUBB 4981 0.061 0.46 YES
35 CDC25A CDC25A CDC25A 5006 0.061 0.47 YES
36 HAUS2 HAUS2 HAUS2 5022 0.06 0.48 YES
37 NUMA1 NUMA1 NUMA1 5057 0.06 0.49 YES
38 PAFAH1B1 PAFAH1B1 PAFAH1B1 5068 0.059 0.5 YES
39 YWHAE YWHAE YWHAE 5219 0.056 0.5 YES
40 CEP72 CEP72 CEP72 5224 0.056 0.51 YES
41 CEP63 CEP63 CEP63 5345 0.054 0.51 YES
42 TUBGCP6 TUBGCP6 TUBGCP6 5473 0.052 0.51 YES
43 E2F3 E2F3 E2F3 5520 0.051 0.52 YES
44 DYNLL1 DYNLL1 DYNLL1 5698 0.048 0.52 YES
45 E2F1 E2F1 E2F1 5954 0.043 0.51 YES
46 SDCCAG8 SDCCAG8 SDCCAG8 5966 0.043 0.52 YES
47 CDK7 CDK7 CDK7 6142 0.04 0.52 YES
48 CEP135 CEP135 CEP135 6201 0.039 0.52 YES
49 CENPJ CENPJ CENPJ 6424 0.036 0.52 YES
50 HSP90AA1 HSP90AA1 HSP90AA1 6490 0.035 0.52 YES
51 CDC25C CDC25C CDC25C 6534 0.034 0.52 YES
52 CEP192 CEP192 CEP192 6757 0.031 0.52 NO
53 DCTN2 DCTN2 DCTN2 6936 0.028 0.51 NO
54 CDC25B CDC25B CDC25B 6968 0.028 0.51 NO
55 CDK2 CDK2 CDK2 6985 0.027 0.52 NO
56 DYNC1I2 DYNC1I2 DYNC1I2 7206 0.024 0.51 NO
57 CEP290 CEP290 CEP290 7371 0.022 0.51 NO
58 DCTN3 DCTN3 DCTN3 7513 0.02 0.5 NO
59 AKAP9 AKAP9 AKAP9 7765 0.016 0.49 NO
60 SSNA1 SSNA1 SSNA1 7859 0.015 0.49 NO
61 ACTR1A ACTR1A ACTR1A 8080 0.012 0.48 NO
62 TUBGCP3 TUBGCP3 TUBGCP3 8110 0.012 0.48 NO
63 MAPRE1 MAPRE1 MAPRE1 8582 0.0052 0.46 NO
64 TUBGCP2 TUBGCP2 TUBGCP2 8687 0.0038 0.45 NO
65 PRKACA PRKACA PRKACA 9387 -0.0067 0.41 NO
66 PPP2R1A PPP2R1A PPP2R1A 9593 -0.0095 0.4 NO
67 CSNK1D CSNK1D CSNK1D 9676 -0.011 0.4 NO
68 OFD1 OFD1 OFD1 10597 -0.024 0.36 NO
69 TUBA1A TUBA1A TUBA1A 10787 -0.028 0.35 NO
70 PCM1 PCM1 PCM1 11192 -0.036 0.34 NO
71 CEP57 CEP57 CEP57 11556 -0.042 0.32 NO
72 CCNH CCNH CCNH 12962 -0.072 0.26 NO
73 FGFR1OP FGFR1OP FGFR1OP 13193 -0.078 0.26 NO
74 PRKAR2B PRKAR2B PRKAR2B 15801 -0.19 0.16 NO

Figure S9.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AURORA A PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AURORA A PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TAP63PATHWAY

Table S6.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NINL NINL NINL 1200 0.26 0.013 YES
2 TUBA4A TUBA4A TUBA4A 1878 0.18 0.031 YES
3 PLK4 PLK4 PLK4 2039 0.17 0.073 YES
4 CLASP1 CLASP1 CLASP1 2662 0.13 0.079 YES
5 NEDD1 NEDD1 NEDD1 3045 0.12 0.093 YES
6 CDK1 CDK1 CDK1 3060 0.12 0.13 YES
7 NEK2 NEK2 NEK2 3636 0.095 0.12 YES
8 CEP250 CEP250 CEP250 3782 0.091 0.14 YES
9 YWHAG YWHAG YWHAG 4068 0.082 0.15 YES
10 TUBG1 TUBG1 TUBG1 4174 0.08 0.17 YES
11 CEP164 CEP164 CEP164 4267 0.077 0.19 YES
12 CSNK1E CSNK1E CSNK1E 4282 0.076 0.21 YES
13 CEP70 CEP70 CEP70 4337 0.075 0.23 YES
14 DYNC1H1 DYNC1H1 DYNC1H1 4369 0.074 0.25 YES
15 CDK5RAP2 CDK5RAP2 CDK5RAP2 4376 0.074 0.27 YES
16 CKAP5 CKAP5 CKAP5 4411 0.073 0.29 YES
17 ALMS1 ALMS1 ALMS1 4429 0.073 0.31 YES
18 CETN2 CETN2 CETN2 4433 0.073 0.33 YES
19 DCTN1 DCTN1 DCTN1 4647 0.068 0.34 YES
20 CEP76 CEP76 CEP76 4689 0.068 0.36 YES
21 PCNT PCNT PCNT 4725 0.067 0.37 YES
22 AZI1 AZI1 AZI1 4807 0.065 0.39 YES
23 PLK1 PLK1 PLK1 4956 0.062 0.4 YES
24 TUBB TUBB TUBB 4981 0.061 0.42 YES
25 HAUS2 HAUS2 HAUS2 5022 0.06 0.43 YES
26 PAFAH1B1 PAFAH1B1 PAFAH1B1 5068 0.059 0.45 YES
27 YWHAE YWHAE YWHAE 5219 0.056 0.46 YES
28 CEP72 CEP72 CEP72 5224 0.056 0.47 YES
29 CEP63 CEP63 CEP63 5345 0.054 0.48 YES
30 DYNLL1 DYNLL1 DYNLL1 5698 0.048 0.48 NO
31 SDCCAG8 SDCCAG8 SDCCAG8 5966 0.043 0.47 NO
32 CEP135 CEP135 CEP135 6201 0.039 0.47 NO
33 CENPJ CENPJ CENPJ 6424 0.036 0.47 NO
34 HSP90AA1 HSP90AA1 HSP90AA1 6490 0.035 0.48 NO
35 CEP192 CEP192 CEP192 6757 0.031 0.47 NO
36 DCTN2 DCTN2 DCTN2 6936 0.028 0.47 NO
37 DYNC1I2 DYNC1I2 DYNC1I2 7206 0.024 0.46 NO
38 CEP290 CEP290 CEP290 7371 0.022 0.46 NO
39 DCTN3 DCTN3 DCTN3 7513 0.02 0.46 NO
40 AKAP9 AKAP9 AKAP9 7765 0.016 0.45 NO
41 SSNA1 SSNA1 SSNA1 7859 0.015 0.45 NO
42 ACTR1A ACTR1A ACTR1A 8080 0.012 0.44 NO
43 MAPRE1 MAPRE1 MAPRE1 8582 0.0052 0.42 NO
44 PRKACA PRKACA PRKACA 9387 -0.0067 0.38 NO
45 PPP2R1A PPP2R1A PPP2R1A 9593 -0.0095 0.37 NO
46 CSNK1D CSNK1D CSNK1D 9676 -0.011 0.37 NO
47 OFD1 OFD1 OFD1 10597 -0.024 0.32 NO
48 TUBA1A TUBA1A TUBA1A 10787 -0.028 0.32 NO
49 PCM1 PCM1 PCM1 11192 -0.036 0.31 NO
50 CEP57 CEP57 CEP57 11556 -0.042 0.3 NO
51 FGFR1OP FGFR1OP FGFR1OP 13193 -0.078 0.24 NO
52 PRKAR2B PRKAR2B PRKAR2B 15801 -0.19 0.16 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TAP63PATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: PID TAP63PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID P53REGULATIONPATHWAY

Table S7.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SPHK1 SPHK1 SPHK1 717 0.37 0.24 YES
2 KIFC3 KIFC3 KIFC3 2268 0.16 0.28 YES
3 CCT4 CCT4 CCT4 4290 0.076 0.23 YES
4 CCT5 CCT5 CCT5 4358 0.074 0.28 YES
5 USP11 USP11 USP11 5360 0.054 0.27 YES
6 KIF13A KIF13A KIF13A 5679 0.048 0.29 YES
7 CCT6A CCT6A CCT6A 5952 0.043 0.31 YES
8 TCP1 TCP1 TCP1 5990 0.042 0.34 YES
9 FBXW2 FBXW2 FBXW2 6051 0.041 0.37 YES
10 FKBP9 FKBP9 FKBP9 6435 0.035 0.37 YES
11 FBXW7 FBXW7 FBXW7 6452 0.035 0.4 YES
12 FBXW4 FBXW4 FBXW4 6454 0.035 0.43 YES
13 CCT7 CCT7 CCT7 6476 0.035 0.45 YES
14 CCT8 CCT8 CCT8 6778 0.03 0.46 YES
15 CCT2 CCT2 CCT2 7223 0.024 0.45 YES
16 CCT3 CCT3 CCT3 7294 0.023 0.47 YES
17 XRN2 XRN2 XRN2 7857 0.015 0.45 NO
18 NOP56 NOP56 NOP56 7878 0.015 0.46 NO
19 FBXL3 FBXL3 FBXL3 8160 0.011 0.45 NO
20 LONP2 LONP2 LONP2 9325 -0.0056 0.39 NO
21 FBXL5 FBXL5 FBXL5 9666 -0.011 0.38 NO
22 FBXO6 FBXO6 FBXO6 9857 -0.013 0.38 NO
23 ARFGEF2 ARFGEF2 ARFGEF2 9952 -0.015 0.39 NO
24 AP3M1 AP3M1 AP3M1 10209 -0.018 0.39 NO
25 FBXW5 FBXW5 FBXW5 10912 -0.03 0.38 NO
26 FBXO4 FBXO4 FBXO4 12209 -0.055 0.35 NO

Figure S13.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P53REGULATIONPATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: PID P53REGULATIONPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS

Table S8.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NUP155 NUP155 NUP155 2534 0.14 -0.064 YES
2 NUP210 NUP210 NUP210 2769 0.13 -0.011 YES
3 NUP153 NUP153 NUP153 3176 0.11 0.024 YES
4 NUP205 NUP205 NUP205 3371 0.1 0.067 YES
5 NUP188 NUP188 NUP188 3377 0.1 0.12 YES
6 NUP93 NUP93 NUP93 4067 0.082 0.12 YES
7 NUP37 NUP37 NUP37 4377 0.074 0.15 YES
8 CPSF3 CPSF3 CPSF3 4393 0.074 0.18 YES
9 NUP107 NUP107 NUP107 4416 0.073 0.22 YES
10 NCBP2 NCBP2 NCBP2 4697 0.068 0.24 YES
11 NUP54 NUP54 NUP54 4760 0.066 0.27 YES
12 CPSF2 CPSF2 CPSF2 4938 0.062 0.29 YES
13 NUP50 NUP50 NUP50 5144 0.058 0.31 YES
14 NUP85 NUP85 NUP85 5227 0.056 0.33 YES
15 RBM8A RBM8A RBM8A 5338 0.054 0.36 YES
16 SEH1L SEH1L SEH1L 5410 0.053 0.38 YES
17 NUP133 NUP133 NUP133 5422 0.053 0.4 YES
18 EIF4E EIF4E EIF4E 5968 0.043 0.4 YES
19 RAE1 RAE1 RAE1 5975 0.043 0.42 YES
20 NXF1 NXF1 NXF1 6070 0.041 0.44 YES
21 NUP214 NUP214 NUP214 6151 0.04 0.45 YES
22 TPR TPR TPR 6362 0.036 0.46 YES
23 SRRM1 SRRM1 SRRM1 6513 0.034 0.47 YES
24 DHX38 DHX38 DHX38 6622 0.032 0.48 YES
25 SLBP SLBP SLBP 6688 0.032 0.49 YES
26 UPF3B UPF3B UPF3B 6690 0.032 0.51 YES
27 NUPL1 NUPL1 NUPL1 6798 0.03 0.52 YES
28 POM121 POM121 POM121 6829 0.03 0.53 YES
29 U2AF1 U2AF1 U2AF1 7226 0.024 0.52 YES
30 RANBP2 RANBP2 RANBP2 7280 0.023 0.53 YES
31 RNPS1 RNPS1 RNPS1 7288 0.023 0.54 YES
32 THOC4 THOC4 THOC4 7312 0.022 0.55 YES
33 NUP35 NUP35 NUP35 7690 0.017 0.54 NO
34 NUP88 NUP88 NUP88 7789 0.016 0.54 NO
35 NUPL2 NUPL2 NUPL2 7986 0.014 0.54 NO
36 NCBP1 NCBP1 NCBP1 8417 0.0073 0.52 NO
37 NFX1 NFX1 NFX1 8607 0.005 0.51 NO
38 AAAS AAAS AAAS 8940 0.00012 0.5 NO
39 CPSF1 CPSF1 CPSF1 8964 -0.00024 0.49 NO
40 NUP62 NUP62 NUP62 9120 -0.0024 0.49 NO
41 NUP43 NUP43 NUP43 9343 -0.006 0.48 NO
42 U2AF2 U2AF2 U2AF2 9532 -0.0086 0.47 NO
43 CDC40 CDC40 CDC40 9685 -0.011 0.47 NO
44 MAGOH MAGOH MAGOH 10749 -0.027 0.43 NO

Figure S15.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME MEMBRANE TRAFFICKING

Table S9.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PKP1 PKP1 PKP1 6 1.2 0.19 YES
2 DSG3 DSG3 DSG3 76 0.91 0.34 YES
3 DSG1 DSG1 DSG1 103 0.84 0.47 YES
4 DSP DSP DSP 775 0.36 0.49 YES
5 PLEC PLEC PLEC 3431 0.1 0.37 NO
6 FNTA FNTA FNTA 3614 0.096 0.37 NO
7 LMNA LMNA LMNA 4638 0.069 0.33 NO
8 TJP1 TJP1 TJP1 5056 0.06 0.32 NO
9 CDH1 CDH1 CDH1 5277 0.056 0.31 NO
10 PTK2 PTK2 PTK2 6153 0.04 0.27 NO
11 DBNL DBNL DBNL 6174 0.04 0.28 NO
12 MST4 MST4 MST4 6182 0.04 0.28 NO
13 STK24 STK24 STK24 6407 0.036 0.28 NO
14 BCAP31 BCAP31 BCAP31 7278 0.023 0.24 NO
15 ACIN1 ACIN1 ACIN1 7286 0.023 0.24 NO
16 APC APC APC 7462 0.021 0.23 NO
17 MAPT MAPT MAPT 7482 0.02 0.24 NO
18 BIRC2 BIRC2 BIRC2 7538 0.02 0.24 NO
19 CTNNB1 CTNNB1 CTNNB1 8380 0.0079 0.19 NO
20 GSN GSN GSN 8597 0.0051 0.18 NO
21 ROCK1 ROCK1 ROCK1 9198 -0.0037 0.15 NO
22 DSG2 DSG2 DSG2 9412 -0.007 0.14 NO
23 LMNB1 LMNB1 LMNB1 9649 -0.01 0.13 NO
24 CASP3 CASP3 CASP3 11319 -0.038 0.045 NO
25 ADD1 ADD1 ADD1 11431 -0.04 0.045 NO
26 SPTAN1 SPTAN1 SPTAN1 11826 -0.047 0.032 NO
27 PRKCD PRKCD PRKCD 13187 -0.077 -0.029 NO
28 VIM VIM VIM 13310 -0.081 -0.022 NO
29 TJP2 TJP2 TJP2 13363 -0.082 -0.012 NO
30 CASP8 CASP8 CASP8 13463 -0.085 -0.0031 NO
31 CASP7 CASP7 CASP7 13694 -0.092 -0.00059 NO
32 LOC647859 LOC647859 LOC647859 14394 -0.12 -0.019 NO
33 PRKCQ PRKCQ PRKCQ 14552 -0.12 -0.0074 NO
34 SATB1 SATB1 SATB1 14838 -0.14 -0.00061 NO
35 CASP6 CASP6 CASP6 16379 -0.23 -0.046 NO
36 BMX BMX BMX 16919 -0.28 -0.03 NO
37 OCLN OCLN OCLN 17601 -0.35 -0.0097 NO
38 GAS2 GAS2 GAS2 18082 -0.43 0.034 NO

Figure S17.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME MEMBRANE TRAFFICKING.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MEMBRANE TRAFFICKING, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

Table S10.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 JUB JUB JUB 1045 0.29 0.069 YES
2 CENPA CENPA CENPA 1584 0.22 0.13 YES
3 BIRC5 BIRC5 BIRC5 1733 0.2 0.21 YES
4 DLGAP5 DLGAP5 DLGAP5 2163 0.16 0.26 YES
5 AURKB AURKB AURKB 2446 0.14 0.3 YES
6 NDEL1 NDEL1 NDEL1 2669 0.13 0.35 YES
7 BRCA1 BRCA1 BRCA1 3007 0.12 0.38 YES
8 TPX2 TPX2 TPX2 3534 0.098 0.39 YES
9 FZR1 FZR1 FZR1 3589 0.097 0.43 YES
10 GSK3B GSK3B GSK3B 4133 0.08 0.44 YES
11 GIT1 GIT1 GIT1 4319 0.075 0.46 YES
12 CKAP5 CKAP5 CKAP5 4411 0.073 0.49 YES
13 TACC3 TACC3 TACC3 4941 0.062 0.48 YES
14 RAN RAN RAN 5005 0.061 0.51 YES
15 RASA1 RASA1 RASA1 5015 0.06 0.53 YES
16 NFKBIA NFKBIA NFKBIA 5617 0.049 0.52 NO
17 GADD45A GADD45A GADD45A 6423 0.036 0.49 NO
18 CDC25B CDC25B CDC25B 6968 0.028 0.48 NO
19 MDM2 MDM2 MDM2 7999 0.014 0.43 NO
20 PPP2R5D PPP2R5D PPP2R5D 8476 0.0064 0.4 NO
21 AKT1 AKT1 AKT1 8502 0.0061 0.4 NO
22 AURKA AURKA AURKA 8652 0.0044 0.4 NO
23 PRKACA PRKACA PRKACA 9387 -0.0067 0.36 NO
24 OAZ1 OAZ1 OAZ1 9577 -0.0093 0.36 NO
25 AURKAIP1 AURKAIP1 AURKAIP1 9887 -0.014 0.35 NO
26 PAK1 PAK1 PAK1 10068 -0.016 0.34 NO
27 ARHGEF7 ARHGEF7 ARHGEF7 10643 -0.025 0.32 NO
28 TDRD7 TDRD7 TDRD7 10766 -0.028 0.33 NO
29 TP53 TP53 TP53 11418 -0.039 0.31 NO
30 TACC1 TACC1 TACC1 13048 -0.074 0.25 NO
31 CPEB1 CPEB1 CPEB1 14354 -0.12 0.23 NO

Figure S19.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus2 enriched pathways

Table 4.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.56 1.8 0.032 0.33 0.64 0.72 0.28 0.52 0.097 0.079
KEGG PENTOSE PHOSPHATE PATHWAY 27 genes.ES.table 0.63 1.9 0.0021 0.41 0.38 0.18 0.078 0.17 0 0.096
KEGG FRUCTOSE AND MANNOSE METABOLISM 34 genes.ES.table 0.66 2.1 0 0.18 0.084 0.38 0.11 0.34 0 0.043
KEGG SELENOAMINO ACID METABOLISM 26 genes.ES.table 0.53 1.6 0.022 0.42 0.9 0.42 0.17 0.35 0.22 0.11
KEGG SPHINGOLIPID METABOLISM 39 genes.ES.table 0.56 1.8 0.012 0.33 0.71 0.33 0.1 0.3 0.11 0.08
KEGG PYRUVATE METABOLISM 38 genes.ES.table 0.5 1.7 0.016 0.39 0.88 0.34 0.17 0.28 0.18 0.099
KEGG BUTANOATE METABOLISM 31 genes.ES.table 0.64 1.9 0 0.29 0.46 0.48 0.16 0.41 0 0.067
KEGG AMINOACYL TRNA BIOSYNTHESIS 41 genes.ES.table 0.56 1.9 0.016 0.33 0.45 0.58 0.3 0.41 0 0.075
KEGG BASE EXCISION REPAIR 33 genes.ES.table 0.55 1.8 0.027 0.34 0.7 0.48 0.29 0.34 0.11 0.079
KEGG PEROXISOME 76 genes.ES.table 0.6 2.1 0 0.1 0.094 0.47 0.18 0.39 0 0.025
genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table S11.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ALDOB ALDOB ALDOB 77 0.56 0.14 YES
2 FBP1 FBP1 FBP1 336 0.39 0.22 YES
3 GMDS GMDS GMDS 529 0.32 0.29 YES
4 FBP2 FBP2 FBP2 709 0.27 0.35 YES
5 KHK KHK KHK 846 0.25 0.41 YES
6 PFKFB2 PFKFB2 PFKFB2 909 0.24 0.46 YES
7 AKR1B10 AKR1B10 AKR1B10 1331 0.18 0.49 YES
8 TSTA3 TSTA3 TSTA3 1382 0.18 0.53 YES
9 SORD SORD SORD 1780 0.14 0.54 YES
10 FUK FUK FUK 1799 0.14 0.57 YES
11 GMPPA GMPPA GMPPA 1964 0.13 0.6 YES
12 PMM2 PMM2 PMM2 1982 0.13 0.63 YES
13 GMPPB GMPPB GMPPB 2041 0.12 0.66 YES
14 HK2 HK2 HK2 5038 0.041 0.51 NO
15 PFKL PFKL PFKL 5320 0.036 0.5 NO
16 FPGT FPGT FPGT 5935 0.028 0.48 NO
17 PHPT1 PHPT1 PHPT1 6001 0.027 0.48 NO
18 MPI MPI MPI 6052 0.026 0.48 NO
19 TPI1 TPI1 TPI1 7328 0.011 0.42 NO
20 ALDOA ALDOA ALDOA 7450 0.0096 0.41 NO
21 PFKP PFKP PFKP 7494 0.0091 0.41 NO
22 MTMR6 MTMR6 MTMR6 7525 0.0088 0.42 NO
23 PFKFB3 PFKFB3 PFKFB3 8721 -0.005 0.35 NO
24 MTMR2 MTMR2 MTMR2 9871 -0.019 0.3 NO
25 HK3 HK3 HK3 10724 -0.032 0.26 NO
26 MTMR7 MTMR7 MTMR7 10828 -0.034 0.26 NO
27 PMM1 PMM1 PMM1 11278 -0.041 0.25 NO
28 PFKFB4 PFKFB4 PFKFB4 11413 -0.044 0.25 NO
29 PFKM PFKM PFKM 11938 -0.052 0.24 NO
30 ALDOC ALDOC ALDOC 12126 -0.055 0.24 NO
31 MTMR1 MTMR1 MTMR1 12956 -0.074 0.21 NO
32 PFKFB1 PFKFB1 PFKFB1 13197 -0.08 0.22 NO
33 AKR1B1 AKR1B1 AKR1B1 15016 -0.14 0.16 NO
34 HK1 HK1 HK1 15269 -0.16 0.18 NO

Figure S21.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table S12.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SLC27A2 SLC27A2 SLC27A2 338 0.39 0.037 YES
2 FAR2 FAR2 FAR2 427 0.35 0.082 YES
3 NOS2 NOS2 NOS2 493 0.33 0.12 YES
4 ACSL5 ACSL5 ACSL5 521 0.32 0.17 YES
5 AGXT AGXT AGXT 570 0.31 0.21 YES
6 BAAT BAAT BAAT 588 0.31 0.25 YES
7 EPHX2 EPHX2 EPHX2 1129 0.21 0.25 YES
8 DECR2 DECR2 DECR2 1189 0.2 0.28 YES
9 PEX11A PEX11A PEX11A 1344 0.18 0.29 YES
10 PECR PECR PECR 1352 0.18 0.32 YES
11 PXMP2 PXMP2 PXMP2 1391 0.18 0.34 YES
12 XDH XDH XDH 1449 0.17 0.36 YES
13 PEX11G PEX11G PEX11G 1466 0.17 0.38 YES
14 PEX7 PEX7 PEX7 1476 0.17 0.41 YES
15 PHYH PHYH PHYH 1556 0.16 0.42 YES
16 IDH1 IDH1 IDH1 1677 0.15 0.44 YES
17 AMACR AMACR AMACR 1745 0.14 0.46 YES
18 ABCD3 ABCD3 ABCD3 1914 0.13 0.47 YES
19 NUDT12 NUDT12 NUDT12 2386 0.11 0.46 YES
20 HAO2 HAO2 HAO2 2535 0.099 0.46 YES
21 HMGCL HMGCL HMGCL 2544 0.099 0.47 YES
22 ACAA1 ACAA1 ACAA1 2597 0.096 0.48 YES
23 GSTK1 GSTK1 GSTK1 2621 0.095 0.5 YES
24 SCP2 SCP2 SCP2 2660 0.094 0.51 YES
25 HACL1 HACL1 HACL1 2672 0.094 0.52 YES
26 ACOT8 ACOT8 ACOT8 2715 0.092 0.53 YES
27 EHHADH EHHADH EHHADH 2875 0.087 0.54 YES
28 IDH2 IDH2 IDH2 2934 0.084 0.54 YES
29 MLYCD MLYCD MLYCD 3068 0.081 0.55 YES
30 PIPOX PIPOX PIPOX 3112 0.08 0.56 YES
31 ACOX1 ACOX1 ACOX1 3146 0.079 0.57 YES
32 PEX1 PEX1 PEX1 3300 0.075 0.57 YES
33 PEX16 PEX16 PEX16 3356 0.073 0.58 YES
34 ACOX2 ACOX2 ACOX2 3393 0.072 0.58 YES
35 CAT CAT CAT 3431 0.071 0.59 YES
36 PXMP4 PXMP4 PXMP4 3466 0.07 0.6 YES
37 PEX11B PEX11B PEX11B 3698 0.065 0.6 NO
38 HSD17B4 HSD17B4 HSD17B4 3829 0.063 0.6 NO
39 SOD1 SOD1 SOD1 4096 0.057 0.59 NO
40 ABCD1 ABCD1 ABCD1 4147 0.056 0.6 NO
41 PEX2 PEX2 PEX2 4394 0.051 0.59 NO
42 GNPAT GNPAT GNPAT 4617 0.047 0.59 NO
43 DAO DAO DAO 4837 0.044 0.58 NO
44 ABCD4 ABCD4 ABCD4 4849 0.043 0.59 NO
45 CRAT CRAT CRAT 4877 0.043 0.59 NO
46 PEX6 PEX6 PEX6 5410 0.035 0.57 NO
47 PRDX5 PRDX5 PRDX5 5420 0.035 0.57 NO
48 ACSL3 ACSL3 ACSL3 5455 0.034 0.57 NO
49 FAR1 FAR1 FAR1 5958 0.028 0.55 NO
50 PRDX1 PRDX1 PRDX1 6220 0.024 0.54 NO
51 PEX13 PEX13 PEX13 6499 0.02 0.53 NO
52 ECH1 ECH1 ECH1 6915 0.015 0.51 NO
53 PEX14 PEX14 PEX14 7030 0.014 0.5 NO
54 AGPS AGPS AGPS 7253 0.012 0.49 NO
55 PMVK PMVK PMVK 7422 0.01 0.49 NO
56 PEX26 PEX26 PEX26 7501 0.009 0.48 NO
57 MVK MVK MVK 7859 0.0049 0.46 NO
58 ACOX3 ACOX3 ACOX3 8505 -0.0023 0.43 NO
59 PEX3 PEX3 PEX3 8968 -0.0084 0.41 NO
60 PEX5 PEX5 PEX5 8984 -0.0086 0.41 NO
61 ACSL4 ACSL4 ACSL4 9187 -0.011 0.4 NO
62 PEX10 PEX10 PEX10 9249 -0.012 0.4 NO
63 SLC25A17 SLC25A17 SLC25A17 9999 -0.021 0.36 NO
64 DHRS4 DHRS4 DHRS4 10017 -0.021 0.36 NO
65 PEX19 PEX19 PEX19 10034 -0.022 0.36 NO
66 PEX12 PEX12 PEX12 10798 -0.033 0.33 NO
67 ACSL6 ACSL6 ACSL6 10820 -0.034 0.33 NO
68 NUDT19 NUDT19 NUDT19 11045 -0.037 0.32 NO
69 DDO DDO DDO 11132 -0.039 0.32 NO
70 MPV17L MPV17L MPV17L 11156 -0.039 0.33 NO
71 MPV17 MPV17 MPV17 11439 -0.044 0.32 NO
72 SOD2 SOD2 SOD2 12096 -0.054 0.29 NO
73 PAOX PAOX PAOX 12331 -0.059 0.29 NO
74 ACSL1 ACSL1 ACSL1 14380 -0.12 0.2 NO
75 ABCD2 ABCD2 ABCD2 14754 -0.13 0.19 NO
76 CROT CROT CROT 14951 -0.14 0.2 NO

Figure S23.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table S13.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ALDOB ALDOB ALDOB 77 0.56 0.24 YES
2 FBP1 FBP1 FBP1 336 0.39 0.39 YES
3 FBP2 FBP2 FBP2 709 0.27 0.49 YES
4 RBKS RBKS RBKS 906 0.24 0.58 YES
5 RPIA RPIA RPIA 1463 0.17 0.63 YES
6 LOC729020 LOC729020 LOC729020 3075 0.081 0.57 NO
7 TKTL1 TKTL1 TKTL1 5013 0.041 0.49 NO
8 TKTL2 TKTL2 TKTL2 5231 0.038 0.49 NO
9 PFKL PFKL PFKL 5320 0.036 0.5 NO
10 RPE RPE RPE 5339 0.036 0.52 NO
11 PRPS2 PRPS2 PRPS2 5866 0.029 0.5 NO
12 GPI GPI GPI 7102 0.013 0.44 NO
13 TALDO1 TALDO1 TALDO1 7181 0.012 0.44 NO
14 ALDOA ALDOA ALDOA 7450 0.0096 0.44 NO
15 PFKP PFKP PFKP 7494 0.0091 0.44 NO
16 TKT TKT TKT 7948 0.0038 0.41 NO
17 DERA DERA DERA 8275 0.00028 0.4 NO
18 PGM1 PGM1 PGM1 8806 -0.0062 0.37 NO
19 PGLS PGLS PGLS 9140 -0.01 0.36 NO
20 PRPS1L1 PRPS1L1 PRPS1L1 9756 -0.018 0.33 NO
21 PGD PGD PGD 10600 -0.03 0.3 NO
22 PGM2 PGM2 PGM2 10812 -0.034 0.3 NO
23 PRPS1 PRPS1 PRPS1 10948 -0.036 0.31 NO
24 PFKM PFKM PFKM 11938 -0.052 0.28 NO
25 H6PD H6PD H6PD 12006 -0.053 0.3 NO
26 ALDOC ALDOC ALDOC 12126 -0.055 0.32 NO
27 G6PD G6PD G6PD 13266 -0.082 0.29 NO

Figure S25.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

Table S14.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MARS2 MARS2 MARS2 1816 0.14 -0.026 YES
2 NARS2 NARS2 NARS2 2618 0.095 -0.02 YES
3 DARS2 DARS2 DARS2 2698 0.093 0.024 YES
4 AIMP2 AIMP2 AIMP2 2707 0.092 0.071 YES
5 QARS QARS QARS 2970 0.084 0.1 YES
6 PPA1 PPA1 PPA1 3159 0.079 0.13 YES
7 PPA2 PPA2 PPA2 3168 0.079 0.17 YES
8 AARS2 AARS2 AARS2 3232 0.077 0.21 YES
9 PARS2 PARS2 PARS2 3453 0.07 0.23 YES
10 FARSB FARSB FARSB 3638 0.066 0.26 YES
11 WARS2 WARS2 WARS2 3810 0.063 0.28 YES
12 AIMP1 AIMP1 AIMP1 3837 0.062 0.31 YES
13 NARS NARS NARS 3897 0.061 0.34 YES
14 EEF1E1 EEF1E1 EEF1E1 3927 0.06 0.37 YES
15 CARS2 CARS2 CARS2 4240 0.054 0.38 YES
16 EARS2 EARS2 EARS2 4305 0.052 0.4 YES
17 LARS2 LARS2 LARS2 4337 0.052 0.43 YES
18 IARS2 IARS2 IARS2 4338 0.052 0.46 YES
19 TARS2 TARS2 TARS2 4340 0.052 0.48 YES
20 RARS RARS RARS 4411 0.051 0.5 YES
21 SARS2 SARS2 SARS2 4418 0.05 0.53 YES
22 VARS VARS VARS 4492 0.049 0.55 YES
23 HARS2 HARS2 HARS2 4604 0.047 0.57 YES
24 EPRS EPRS EPRS 4766 0.045 0.58 YES
25 VARS2 VARS2 VARS2 4783 0.045 0.61 YES
26 GARS GARS GARS 5440 0.034 0.59 NO
27 FARSA FARSA FARSA 5470 0.034 0.61 NO
28 CARS CARS CARS 6460 0.021 0.56 NO
29 KARS KARS KARS 6850 0.016 0.55 NO
30 YARS2 YARS2 YARS2 7079 0.014 0.55 NO
31 YARS YARS YARS 7123 0.013 0.55 NO
32 RARS2 RARS2 RARS2 7316 0.011 0.55 NO
33 IARS IARS IARS 7456 0.0095 0.54 NO
34 SARS SARS SARS 7767 0.0058 0.53 NO
35 MARS MARS MARS 7898 0.0043 0.52 NO
36 TARS TARS TARS 8335 -0.00036 0.5 NO
37 HARS HARS HARS 8617 -0.0037 0.49 NO
38 FARS2 FARS2 FARS2 8908 -0.0077 0.48 NO
39 AARS AARS AARS 9144 -0.01 0.47 NO
40 LARS LARS LARS 9305 -0.012 0.47 NO
41 DARS DARS DARS 10477 -0.028 0.42 NO
42 WARS WARS WARS 11341 -0.042 0.4 NO

Figure S27.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SELENOAMINO ACID METABOLISM.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SELENOAMINO ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SPHINGOLIPID METABOLISM

Table S15.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MARS2 MARS2 MARS2 1816 0.14 -0.02 YES
2 SEPSECS SEPSECS SEPSECS 2078 0.12 0.035 YES
3 NARS2 NARS2 NARS2 2618 0.095 0.06 YES
4 DARS2 DARS2 DARS2 2698 0.093 0.11 YES
5 QARS QARS QARS 2970 0.084 0.14 YES
6 AARS2 AARS2 AARS2 3232 0.077 0.17 YES
7 PARS2 PARS2 PARS2 3453 0.07 0.2 YES
8 FARSB FARSB FARSB 3638 0.066 0.23 YES
9 WARS2 WARS2 WARS2 3810 0.063 0.25 YES
10 NARS NARS NARS 3897 0.061 0.28 YES
11 CARS2 CARS2 CARS2 4240 0.054 0.29 YES
12 EARS2 EARS2 EARS2 4305 0.052 0.32 YES
13 LARS2 LARS2 LARS2 4337 0.052 0.35 YES
14 IARS2 IARS2 IARS2 4338 0.052 0.38 YES
15 TARS2 TARS2 TARS2 4340 0.052 0.41 YES
16 RARS RARS RARS 4411 0.051 0.43 YES
17 SARS2 SARS2 SARS2 4418 0.05 0.46 YES
18 VARS VARS VARS 4492 0.049 0.48 YES
19 HARS2 HARS2 HARS2 4604 0.047 0.5 YES
20 EPRS EPRS EPRS 4766 0.045 0.52 YES
21 VARS2 VARS2 VARS2 4783 0.045 0.55 YES
22 GARS GARS GARS 5440 0.034 0.53 YES
23 FARSA FARSA FARSA 5470 0.034 0.55 YES
24 MTFMT MTFMT MTFMT 5612 0.032 0.56 YES
25 CARS CARS CARS 6460 0.021 0.52 NO
26 KARS KARS KARS 6850 0.016 0.51 NO
27 YARS2 YARS2 YARS2 7079 0.014 0.51 NO
28 YARS YARS YARS 7123 0.013 0.51 NO
29 PSTK PSTK PSTK 7304 0.011 0.51 NO
30 RARS2 RARS2 RARS2 7316 0.011 0.52 NO
31 IARS IARS IARS 7456 0.0095 0.51 NO
32 SARS SARS SARS 7767 0.0058 0.5 NO
33 MARS MARS MARS 7898 0.0043 0.5 NO
34 TARS TARS TARS 8335 -0.00036 0.47 NO
35 HARS HARS HARS 8617 -0.0037 0.46 NO
36 FARS2 FARS2 FARS2 8908 -0.0077 0.45 NO
37 AARS AARS AARS 9144 -0.01 0.44 NO
38 LARS LARS LARS 9305 -0.012 0.44 NO
39 DARS DARS DARS 10477 -0.028 0.39 NO
40 WARS WARS WARS 11341 -0.042 0.37 NO
41 TARSL2 TARSL2 TARSL2 11408 -0.043 0.39 NO

Figure S29.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SPHINGOLIPID METABOLISM.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPHINGOLIPID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRUVATE METABOLISM

Table S16.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACSM3 ACSM3 ACSM3 113 0.52 0.15 YES
2 HMGCS2 HMGCS2 HMGCS2 121 0.51 0.3 YES
3 ACSM1 ACSM1 ACSM1 996 0.23 0.32 YES
4 ACADS ACADS ACADS 1211 0.2 0.37 YES
5 AKR1B10 AKR1B10 AKR1B10 1331 0.18 0.41 YES
6 ALDH2 ALDH2 ALDH2 1675 0.15 0.44 YES
7 ABAT ABAT ABAT 1886 0.13 0.47 YES
8 GAD1 GAD1 GAD1 2392 0.11 0.47 YES
9 HADH HADH HADH 2434 0.1 0.5 YES
10 BDH1 BDH1 BDH1 2518 0.1 0.53 YES
11 HMGCL HMGCL HMGCL 2544 0.099 0.56 YES
12 PDHA1 PDHA1 PDHA1 2564 0.098 0.58 YES
13 ECHS1 ECHS1 ECHS1 2650 0.095 0.61 YES
14 EHHADH EHHADH EHHADH 2875 0.087 0.62 YES
15 ACAT2 ACAT2 ACAT2 3041 0.082 0.64 YES
16 HMGCS1 HMGCS1 HMGCS1 3887 0.061 0.61 NO
17 ALDH9A1 ALDH9A1 ALDH9A1 4979 0.041 0.56 NO
18 HADHA HADHA HADHA 5174 0.039 0.56 NO
19 PDHB PDHB PDHB 5216 0.038 0.57 NO
20 ACAT1 ACAT1 ACAT1 5744 0.03 0.55 NO
21 BDH2 BDH2 BDH2 5829 0.029 0.56 NO
22 L2HGDH L2HGDH L2HGDH 5837 0.029 0.57 NO
23 ALDH5A1 ALDH5A1 ALDH5A1 6279 0.024 0.55 NO
24 OXCT2 OXCT2 OXCT2 6885 0.016 0.52 NO
25 ACSM2A ACSM2A ACSM2A 7081 0.014 0.52 NO
26 AACS AACS AACS 7565 0.0081 0.49 NO
27 ALDH3A2 ALDH3A2 ALDH3A2 8576 -0.0031 0.44 NO
28 ALDH7A1 ALDH7A1 ALDH7A1 10103 -0.023 0.36 NO
29 ALDH1B1 ALDH1B1 ALDH1B1 10432 -0.028 0.36 NO
30 ACSM5 ACSM5 ACSM5 15090 -0.15 0.15 NO
31 OXCT1 OXCT1 OXCT1 15216 -0.15 0.19 NO

Figure S31.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PYRUVATE METABOLISM.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table S17.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SUCLG2 SUCLG2 SUCLG2 1419 0.17 -0.05 YES
2 IDH1 IDH1 IDH1 1677 0.15 -0.042 YES
3 SUCLG1 SUCLG1 SUCLG1 2024 0.12 -0.042 YES
4 ATP5G1 ATP5G1 ATP5G1 2205 0.11 -0.035 YES
5 COX5A COX5A COX5A 2431 0.1 -0.032 YES
6 CYCS CYCS CYCS 2525 0.1 -0.022 YES
7 PDHA1 PDHA1 PDHA1 2564 0.098 -0.0091 YES
8 ETFDH ETFDH ETFDH 2657 0.094 -0.000078 YES
9 CYC1 CYC1 CYC1 2770 0.09 0.0072 YES
10 UQCRHL UQCRHL UQCRHL 2777 0.09 0.02 YES
11 ETFA ETFA ETFA 2889 0.086 0.027 YES
12 IDH2 IDH2 IDH2 2934 0.084 0.037 YES
13 UQCRFS1 UQCRFS1 UQCRFS1 2966 0.084 0.048 YES
14 D2HGDH D2HGDH D2HGDH 3047 0.082 0.056 YES
15 NDUFA1 NDUFA1 NDUFA1 3063 0.082 0.067 YES
16 NDUFS2 NDUFS2 NDUFS2 3081 0.081 0.078 YES
17 NDUFA3 NDUFA3 NDUFA3 3133 0.08 0.087 YES
18 UQCRQ UQCRQ UQCRQ 3158 0.079 0.098 YES
19 NDUFA2 NDUFA2 NDUFA2 3172 0.078 0.11 YES
20 UQCRH UQCRH UQCRH 3206 0.078 0.12 YES
21 NDUFA9 NDUFA9 NDUFA9 3215 0.077 0.13 YES
22 COX7B COX7B COX7B 3254 0.076 0.14 YES
23 NDUFC2 NDUFC2 NDUFC2 3305 0.075 0.15 YES
24 NDUFA4 NDUFA4 NDUFA4 3341 0.074 0.16 YES
25 NDUFS3 NDUFS3 NDUFS3 3342 0.074 0.17 YES
26 COX5B COX5B COX5B 3345 0.074 0.18 YES
27 COX6A1 COX6A1 COX6A1 3360 0.073 0.19 YES
28 NDUFV2 NDUFV2 NDUFV2 3387 0.072 0.2 YES
29 SDHB SDHB SDHB 3511 0.069 0.2 YES
30 ETFB ETFB ETFB 3553 0.068 0.21 YES
31 COX6C COX6C COX6C 3590 0.067 0.22 YES
32 ATP5F1 ATP5F1 ATP5F1 3594 0.067 0.23 YES
33 NDUFA7 NDUFA7 NDUFA7 3616 0.067 0.24 YES
34 SDHA SDHA SDHA 3625 0.067 0.24 YES
35 ATP5I ATP5I ATP5I 3630 0.067 0.26 YES
36 IDH3A IDH3A IDH3A 3647 0.066 0.26 YES
37 UQCRC1 UQCRC1 UQCRC1 3659 0.066 0.27 YES
38 ATP5J2 ATP5J2 ATP5J2 3707 0.065 0.28 YES
39 NDUFA5 NDUFA5 NDUFA5 3740 0.064 0.29 YES
40 NDUFB3 NDUFB3 NDUFB3 3762 0.064 0.3 YES
41 UQCRC2 UQCRC2 UQCRC2 3764 0.064 0.31 YES
42 COX6B1 COX6B1 COX6B1 3782 0.064 0.31 YES
43 NDUFB2 NDUFB2 NDUFB2 3789 0.063 0.32 YES
44 ATP5B ATP5B ATP5B 3824 0.063 0.33 YES
45 ATP5C1 ATP5C1 ATP5C1 3835 0.062 0.34 YES
46 NDUFB6 NDUFB6 NDUFB6 3847 0.062 0.35 YES
47 NDUFAB1 NDUFAB1 NDUFAB1 3848 0.062 0.36 YES
48 FH FH FH 3912 0.061 0.36 YES
49 SDHD SDHD SDHD 3924 0.06 0.37 YES
50 NDUFS1 NDUFS1 NDUFS1 3926 0.06 0.38 YES
51 NDUFV1 NDUFV1 NDUFV1 3932 0.06 0.39 YES
52 NDUFB9 NDUFB9 NDUFB9 3937 0.06 0.4 YES
53 IDH3B IDH3B IDH3B 4019 0.058 0.4 YES
54 NDUFA10 NDUFA10 NDUFA10 4112 0.057 0.4 YES
55 ATP5L ATP5L ATP5L 4155 0.056 0.41 YES
56 ATP5D ATP5D ATP5D 4219 0.054 0.42 YES
57 ATP5O ATP5O ATP5O 4241 0.054 0.42 YES
58 NDUFC1 NDUFC1 NDUFC1 4262 0.054 0.43 YES
59 COX8A COX8A COX8A 4269 0.053 0.44 YES
60 COX4I1 COX4I1 COX4I1 4276 0.053 0.44 YES
61 COX7C COX7C COX7C 4304 0.052 0.45 YES
62 SUCLA2 SUCLA2 SUCLA2 4479 0.049 0.45 YES
63 DLD DLD DLD 4506 0.049 0.46 YES
64 MDH2 MDH2 MDH2 4534 0.048 0.46 YES
65 UQCRB UQCRB UQCRB 4569 0.048 0.47 YES
66 PDK4 PDK4 PDK4 4583 0.048 0.47 YES
67 NDUFS6 NDUFS6 NDUFS6 4687 0.046 0.47 YES
68 COX7A2L COX7A2L COX7A2L 4697 0.046 0.48 YES
69 DLAT DLAT DLAT 4795 0.044 0.48 YES
70 IDH3G IDH3G IDH3G 4796 0.044 0.49 YES
71 PDHX PDHX PDHX 4925 0.042 0.49 YES
72 SLC16A1 SLC16A1 SLC16A1 4953 0.042 0.49 YES
73 ATP5E ATP5E ATP5E 5041 0.041 0.49 YES
74 SDHC SDHC SDHC 5055 0.041 0.5 YES
75 NDUFB1 NDUFB1 NDUFB1 5129 0.04 0.5 YES
76 UQCR11 UQCR11 UQCR11 5130 0.04 0.51 YES
77 NDUFS7 NDUFS7 NDUFS7 5140 0.039 0.51 YES
78 NDUFA12 NDUFA12 NDUFA12 5143 0.039 0.52 YES
79 BSG BSG BSG 5208 0.038 0.52 YES
80 PDHB PDHB PDHB 5216 0.038 0.53 YES
81 NDUFA6 NDUFA6 NDUFA6 5222 0.038 0.53 YES
82 NDUFA8 NDUFA8 NDUFA8 5265 0.038 0.53 YES
83 NDUFB8 NDUFB8 NDUFB8 5429 0.035 0.53 YES
84 ATP5A1 ATP5A1 ATP5A1 5473 0.034 0.53 YES
85 ACO2 ACO2 ACO2 5494 0.034 0.54 YES
86 NDUFA13 NDUFA13 NDUFA13 5522 0.034 0.54 YES
87 L2HGDH L2HGDH L2HGDH 5837 0.029 0.53 NO
88 CS CS CS 5876 0.029 0.53 NO
89 NDUFB10 NDUFB10 NDUFB10 5999 0.027 0.53 NO
90 PDK2 PDK2 PDK2 6012 0.027 0.53 NO
91 UCP2 UCP2 UCP2 6106 0.026 0.53 NO
92 ATP5H ATP5H ATP5H 6264 0.024 0.52 NO
93 PDP2 PDP2 PDP2 6458 0.021 0.52 NO
94 ATP5J ATP5J ATP5J 6543 0.02 0.52 NO
95 NNT NNT NNT 6751 0.017 0.51 NO
96 NDUFS8 NDUFS8 NDUFS8 6809 0.017 0.51 NO
97 NDUFB7 NDUFB7 NDUFB7 6815 0.017 0.51 NO
98 DLST DLST DLST 6997 0.014 0.5 NO
99 NDUFS5 NDUFS5 NDUFS5 7095 0.013 0.5 NO
100 OGDH OGDH OGDH 7098 0.013 0.5 NO
101 SLC16A3 SLC16A3 SLC16A3 7140 0.013 0.5 NO
102 NDUFB4 NDUFB4 NDUFB4 7296 0.011 0.49 NO
103 NDUFB5 NDUFB5 NDUFB5 8091 0.0024 0.45 NO
104 LDHA LDHA LDHA 8564 -0.003 0.43 NO
105 PDP1 PDP1 PDP1 8868 -0.0071 0.41 NO
106 NDUFV3 NDUFV3 NDUFV3 9087 -0.0098 0.4 NO
107 NDUFS4 NDUFS4 NDUFS4 9120 -0.01 0.4 NO
108 SLC16A8 SLC16A8 SLC16A8 9279 -0.012 0.39 NO
109 NDUFA11 NDUFA11 NDUFA11 9990 -0.021 0.36 NO
110 PDK1 PDK1 PDK1 10272 -0.026 0.35 NO
111 PDPR PDPR PDPR 11526 -0.045 0.29 NO
112 PDK3 PDK3 PDK3 11536 -0.045 0.29 NO
113 UCP3 UCP3 UCP3 12396 -0.061 0.26 NO
114 LDHB LDHB LDHB 14955 -0.14 0.14 NO
115 ADHFE1 ADHFE1 ADHFE1 18212 -0.42 0.028 NO

Figure S33.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BUTANOATE METABOLISM.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BUTANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table S18.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TPK1 TPK1 TPK1 395 0.36 0.065 YES
2 SLC19A3 SLC19A3 SLC19A3 505 0.33 0.14 YES
3 PANK1 PANK1 PANK1 989 0.23 0.16 YES
4 SLC23A1 SLC23A1 SLC23A1 1099 0.21 0.21 YES
5 GSTO2 GSTO2 GSTO2 1280 0.19 0.24 YES
6 RFK RFK RFK 1575 0.16 0.26 YES
7 MOCOS MOCOS MOCOS 1705 0.15 0.29 YES
8 QPRT QPRT QPRT 1895 0.13 0.31 YES
9 CYB5A CYB5A CYB5A 1932 0.13 0.34 YES
10 SLC19A1 SLC19A1 SLC19A1 1959 0.13 0.37 YES
11 ENPP1 ENPP1 ENPP1 1978 0.13 0.4 YES
12 NMNAT1 NMNAT1 NMNAT1 2380 0.11 0.4 YES
13 SLC5A6 SLC5A6 SLC5A6 2493 0.1 0.42 YES
14 DHFR DHFR DHFR 2515 0.1 0.44 YES
15 PPCS PPCS PPCS 3340 0.074 0.41 YES
16 SLC19A2 SLC19A2 SLC19A2 3513 0.069 0.42 YES
17 PANK3 PANK3 PANK3 3576 0.068 0.43 YES
18 PPCDC PPCDC PPCDC 3701 0.065 0.44 YES
19 NADK NADK NADK 3720 0.065 0.46 YES
20 NFS1 NFS1 NFS1 3942 0.06 0.46 YES
21 SHMT1 SHMT1 SHMT1 3950 0.06 0.47 YES
22 GPHN GPHN GPHN 4026 0.058 0.48 YES
23 PNPO PNPO PNPO 4497 0.049 0.47 YES
24 PDXK PDXK PDXK 4683 0.046 0.47 YES
25 MTHFD1 MTHFD1 MTHFD1 4776 0.045 0.48 YES
26 MTHFR MTHFR MTHFR 4805 0.044 0.48 YES
27 COASY COASY COASY 4924 0.042 0.49 YES
28 MOCS3 MOCS3 MOCS3 5005 0.041 0.49 YES
29 FPGS FPGS FPGS 5209 0.038 0.49 NO
30 SLC25A16 SLC25A16 SLC25A16 5428 0.035 0.49 NO
31 SLC46A1 SLC46A1 SLC46A1 5618 0.032 0.48 NO
32 SLC25A32 SLC25A32 SLC25A32 5951 0.028 0.47 NO
33 FLAD1 FLAD1 FLAD1 5975 0.028 0.48 NO
34 FASN FASN FASN 6973 0.015 0.43 NO
35 GSTO1 GSTO1 GSTO1 7599 0.0078 0.4 NO
36 MOCS2 MOCS2 MOCS2 7688 0.0067 0.39 NO
37 NADSYN1 NADSYN1 NADSYN1 8192 0.0012 0.37 NO
38 THTPA THTPA THTPA 8891 -0.0074 0.33 NO
39 NAMPT NAMPT NAMPT 10276 -0.026 0.26 NO
40 PANK2 PANK2 PANK2 10390 -0.027 0.26 NO
41 AASDHPPT AASDHPPT AASDHPPT 10926 -0.035 0.24 NO
42 PANK4 PANK4 PANK4 11134 -0.039 0.24 NO
43 ACP5 ACP5 ACP5 11646 -0.047 0.22 NO
44 NMNAT2 NMNAT2 NMNAT2 12313 -0.059 0.2 NO
45 SLC2A3 SLC2A3 SLC2A3 12837 -0.071 0.19 NO
46 NMNAT3 NMNAT3 NMNAT3 12843 -0.071 0.21 NO
47 CYB5R3 CYB5R3 CYB5R3 12915 -0.073 0.22 NO
48 MOCS1 MOCS1 MOCS1 13997 -0.1 0.19 NO
49 SLC23A2 SLC23A2 SLC23A2 14622 -0.13 0.18 NO
50 SLC2A1 SLC2A1 SLC2A1 15201 -0.15 0.19 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG BASE EXCISION REPAIR

Table S19.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PCK1 PCK1 PCK1 290 0.41 0.16 YES
2 SUCLG2 SUCLG2 SUCLG2 1419 0.17 0.17 YES
3 PCK2 PCK2 PCK2 1653 0.15 0.22 YES
4 IDH1 IDH1 IDH1 1677 0.15 0.28 YES
5 SUCLG1 SUCLG1 SUCLG1 2024 0.12 0.32 YES
6 ACO1 ACO1 ACO1 2265 0.11 0.35 YES
7 PDHA1 PDHA1 PDHA1 2564 0.098 0.38 YES
8 IDH2 IDH2 IDH2 2934 0.084 0.39 YES
9 SDHB SDHB SDHB 3511 0.069 0.39 YES
10 SDHA SDHA SDHA 3625 0.067 0.41 YES
11 IDH3A IDH3A IDH3A 3647 0.066 0.44 YES
12 FH FH FH 3912 0.061 0.45 YES
13 SDHD SDHD SDHD 3924 0.06 0.48 YES
14 IDH3B IDH3B IDH3B 4019 0.058 0.5 YES
15 SUCLA2 SUCLA2 SUCLA2 4479 0.049 0.49 YES
16 DLD DLD DLD 4506 0.049 0.51 YES
17 MDH2 MDH2 MDH2 4534 0.048 0.53 YES
18 DLAT DLAT DLAT 4795 0.044 0.53 YES
19 IDH3G IDH3G IDH3G 4796 0.044 0.55 YES
20 SDHC SDHC SDHC 5055 0.041 0.56 YES
21 PDHB PDHB PDHB 5216 0.038 0.56 YES
22 ACO2 ACO2 ACO2 5494 0.034 0.56 NO
23 CS CS CS 5876 0.029 0.55 NO
24 DLST DLST DLST 6997 0.014 0.5 NO
25 OGDH OGDH OGDH 7098 0.013 0.5 NO
26 ACLY ACLY ACLY 7196 0.012 0.5 NO
27 MDH1 MDH1 MDH1 7505 0.0089 0.49 NO
28 PC PC PC 14669 -0.13 0.16 NO
29 OGDHL OGDHL OGDHL 14946 -0.14 0.2 NO

Figure S37.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASE EXCISION REPAIR.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASE EXCISION REPAIR, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PEROXISOME

Table S20.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GPD1 GPD1 GPD1 30 0.63 0.057 YES
2 SLC44A4 SLC44A4 SLC44A4 85 0.55 0.1 YES
3 PLA2G10 PLA2G10 PLA2G10 157 0.49 0.15 YES
4 ACHE ACHE ACHE 356 0.38 0.17 YES
5 SLC44A3 SLC44A3 SLC44A3 412 0.36 0.2 YES
6 PLA2G4F PLA2G4F PLA2G4F 637 0.29 0.22 YES
7 DGAT2 DGAT2 DGAT2 785 0.26 0.23 YES
8 DGAT1 DGAT1 DGAT1 871 0.24 0.25 YES
9 LPIN2 LPIN2 LPIN2 905 0.24 0.27 YES
10 PLA2G2A PLA2G2A PLA2G2A 907 0.24 0.29 YES
11 PLA2G16 PLA2G16 PLA2G16 935 0.24 0.31 YES
12 PLBD1 PLBD1 PLBD1 1028 0.22 0.33 YES
13 MBOAT1 MBOAT1 MBOAT1 1154 0.2 0.34 YES
14 CHKA CHKA CHKA 1180 0.2 0.36 YES
15 CDS1 CDS1 CDS1 1230 0.19 0.37 YES
16 AGPAT2 AGPAT2 AGPAT2 1267 0.19 0.39 YES
17 CHPT1 CHPT1 CHPT1 1372 0.18 0.4 YES
18 LPCAT4 LPCAT4 LPCAT4 1376 0.18 0.42 YES
19 AGPAT9 AGPAT9 AGPAT9 1393 0.18 0.43 YES
20 PCYT2 PCYT2 PCYT2 1465 0.17 0.44 YES
21 ETNK1 ETNK1 ETNK1 1482 0.17 0.46 YES
22 CRLS1 CRLS1 CRLS1 1824 0.14 0.45 YES
23 LPIN3 LPIN3 LPIN3 1940 0.13 0.46 YES
24 PLA2G2F PLA2G2F PLA2G2F 1952 0.13 0.47 YES
25 PLA2G4A PLA2G4A PLA2G4A 2085 0.12 0.47 YES
26 GPD1L GPD1L GPD1L 2096 0.12 0.48 YES
27 MGLL MGLL MGLL 2196 0.12 0.49 YES
28 AGPAT5 AGPAT5 AGPAT5 2806 0.089 0.47 NO
29 LPCAT3 LPCAT3 LPCAT3 2840 0.088 0.47 NO
30 PNPLA2 PNPLA2 PNPLA2 2885 0.087 0.48 NO
31 GNPAT GNPAT GNPAT 4617 0.047 0.39 NO
32 CEPT1 CEPT1 CEPT1 4930 0.042 0.38 NO
33 EPT1 EPT1 EPT1 5108 0.04 0.37 NO
34 MBOAT7 MBOAT7 MBOAT7 5171 0.039 0.37 NO
35 HADHA HADHA HADHA 5174 0.039 0.37 NO
36 AGPAT6 AGPAT6 AGPAT6 5253 0.038 0.37 NO
37 PLA2G1B PLA2G1B PLA2G1B 5626 0.032 0.36 NO
38 TAZ TAZ TAZ 5655 0.032 0.36 NO
39 SLC44A1 SLC44A1 SLC44A1 6031 0.027 0.34 NO
40 PTDSS2 PTDSS2 PTDSS2 6071 0.026 0.34 NO
41 PLA2G12A PLA2G12A PLA2G12A 6340 0.023 0.33 NO
42 AGPAT1 AGPAT1 AGPAT1 6403 0.022 0.33 NO
43 LPCAT1 LPCAT1 LPCAT1 6514 0.02 0.32 NO
44 LPGAT1 LPGAT1 LPGAT1 6819 0.017 0.31 NO
45 LCLAT1 LCLAT1 LCLAT1 6852 0.016 0.31 NO
46 SLC44A2 SLC44A2 SLC44A2 6976 0.015 0.3 NO
47 PNPLA3 PNPLA3 PNPLA3 7323 0.011 0.28 NO
48 AGPAT3 AGPAT3 AGPAT3 7404 0.01 0.28 NO
49 LPIN1 LPIN1 LPIN1 7455 0.0095 0.28 NO
50 PEMT PEMT PEMT 7511 0.0088 0.28 NO
51 PLA2G6 PLA2G6 PLA2G6 7569 0.0081 0.28 NO
52 PTDSS1 PTDSS1 PTDSS1 7702 0.0066 0.27 NO
53 HADHB HADHB HADHB 7996 0.0033 0.25 NO
54 GPAT2 GPAT2 GPAT2 8532 -0.0026 0.23 NO
55 GPAM GPAM GPAM 9145 -0.01 0.19 NO
56 CDIPT CDIPT CDIPT 9797 -0.018 0.16 NO
57 CHKB CHKB CHKB 9840 -0.019 0.16 NO
58 CDS2 CDS2 CDS2 10545 -0.029 0.12 NO
59 PLA2G3 PLA2G3 PLA2G3 10732 -0.032 0.12 NO
60 PNPLA8 PNPLA8 PNPLA8 11359 -0.043 0.088 NO
61 PLA2G2D PLA2G2D PLA2G2D 11381 -0.043 0.091 NO
62 PLD1 PLD1 PLD1 11444 -0.044 0.092 NO
63 PHOSPHO1 PHOSPHO1 PHOSPHO1 11609 -0.046 0.087 NO
64 PGS1 PGS1 PGS1 11630 -0.047 0.091 NO
65 PLD6 PLD6 PLD6 11892 -0.051 0.081 NO
66 PLD3 PLD3 PLD3 12192 -0.056 0.071 NO
67 PITPNB PITPNB PITPNB 12336 -0.06 0.068 NO
68 GPCPD1 GPCPD1 GPCPD1 12855 -0.071 0.047 NO
69 PCYT1A PCYT1A PCYT1A 13360 -0.084 0.028 NO
70 LPCAT2 LPCAT2 LPCAT2 13928 -0.1 0.0069 NO
71 PLD2 PLD2 PLD2 14429 -0.12 -0.009 NO
72 PLD4 PLD4 PLD4 14688 -0.13 -0.011 NO
73 MBOAT2 MBOAT2 MBOAT2 14719 -0.13 -0.00051 NO
74 PLA2G4D PLA2G4D PLA2G4D 14866 -0.14 0.0042 NO
75 SLC44A5 SLC44A5 SLC44A5 15659 -0.18 -0.022 NO
76 PLA2G4C PLA2G4C PLA2G4C 17047 -0.28 -0.071 NO
77 AGPAT4 AGPAT4 AGPAT4 17208 -0.29 -0.053 NO
78 PLA2G5 PLA2G5 PLA2G5 17777 -0.35 -0.05 NO
79 ETNK2 ETNK2 ETNK2 18474 -0.5 -0.042 NO
80 PCYT1B PCYT1B PCYT1B 18649 -0.59 0.004 NO

Figure S39.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PEROXISOME.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PEROXISOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus3 enriched pathways

Table 5.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG PURINE METABOLISM 155 genes.ES.table 0.44 1.8 0.002 0.17 0.6 0.19 0.15 0.17 0.045 0.034
KEGG TYROSINE METABOLISM 41 genes.ES.table 0.48 1.4 0.094 0.21 1 0.24 0.12 0.21 0.16 0.001
KEGG TRYPTOPHAN METABOLISM 39 genes.ES.table 0.52 1.5 0.024 0.14 0.99 0.26 0.19 0.21 0.091 0.001
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 26 genes.ES.table 0.55 1.5 0.037 0.14 0.99 0.31 0.22 0.24 0.083 0.001
KEGG ABC TRANSPORTERS 44 genes.ES.table 0.53 1.4 0.057 0.18 1 0.2 0.081 0.19 0.12 0.001
KEGG MAPK SIGNALING PATHWAY 257 genes.ES.table 0.48 1.8 0.0042 0.15 0.66 0.31 0.22 0.24 0.045 0.032
KEGG ERBB SIGNALING PATHWAY 87 genes.ES.table 0.38 1.5 0.038 0.15 1 0.18 0.16 0.16 0.094 0.001
KEGG CALCIUM SIGNALING PATHWAY 176 genes.ES.table 0.62 1.7 0 0.13 0.76 0.49 0.22 0.39 0.043 0.024
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 243 genes.ES.table 0.53 1.4 0.095 0.2 1 0.53 0.25 0.4 0.14 0.001
KEGG CHEMOKINE SIGNALING PATHWAY 185 genes.ES.table 0.57 1.6 0.028 0.12 0.94 0.47 0.26 0.35 0.06 0.007
genes ES table in pathway: KEGG PURINE METABOLISM

Table S21.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IGF1 IGF1 IGF1 84 0.82 0.12 YES
2 FIGF FIGF FIGF 736 0.53 0.17 YES
3 PIK3CG PIK3CG PIK3CG 947 0.49 0.23 YES
4 PRKAA2 PRKAA2 PRKAA2 1283 0.43 0.28 YES
5 PIK3R5 PIK3R5 PIK3R5 1288 0.43 0.35 YES
6 AKT3 AKT3 AKT3 1433 0.41 0.4 YES
7 VEGFC VEGFC VEGFC 1615 0.39 0.45 YES
8 RPS6KA6 RPS6KA6 RPS6KA6 1749 0.36 0.5 YES
9 CAB39L CAB39L CAB39L 2075 0.32 0.53 YES
10 PIK3CD PIK3CD PIK3CD 2911 0.24 0.53 YES
11 RPS6KA2 RPS6KA2 RPS6KA2 3385 0.2 0.53 YES
12 PIK3R1 PIK3R1 PIK3R1 3717 0.18 0.54 YES
13 VEGFB VEGFB VEGFB 3916 0.16 0.56 YES
14 ULK2 ULK2 ULK2 4011 0.16 0.57 YES
15 PIK3R3 PIK3R3 PIK3R3 4769 0.12 0.55 NO
16 PGF PGF PGF 6708 0.055 0.46 NO
17 AKT2 AKT2 AKT2 7538 0.039 0.42 NO
18 EIF4B EIF4B EIF4B 7692 0.036 0.42 NO
19 STRADA STRADA STRADA 7717 0.036 0.42 NO
20 TSC2 TSC2 TSC2 8168 0.028 0.4 NO
21 RPS6 RPS6 RPS6 8253 0.027 0.4 NO
22 PDPK1 PDPK1 PDPK1 8498 0.022 0.39 NO
23 RPS6KA3 RPS6KA3 RPS6KA3 8635 0.021 0.39 NO
24 PIK3CA PIK3CA PIK3CA 8702 0.02 0.39 NO
25 RPTOR RPTOR RPTOR 9487 0.0075 0.35 NO
26 ULK1 ULK1 ULK1 9741 0.0039 0.33 NO
27 BRAF BRAF BRAF 9777 0.0036 0.33 NO
28 TSC1 TSC1 TSC1 9862 0.0024 0.33 NO
29 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.31 NO
30 RICTOR RICTOR RICTOR 10240 -0.0028 0.31 NO
31 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.3 NO
32 MLST8 MLST8 MLST8 10365 -0.0046 0.3 NO
33 PRKAA1 PRKAA1 PRKAA1 10399 -0.0051 0.3 NO
34 AKT1 AKT1 AKT1 10625 -0.0084 0.29 NO
35 STK11 STK11 STK11 11118 -0.015 0.27 NO
36 RHEB RHEB RHEB 11220 -0.016 0.26 NO
37 RPS6KB1 RPS6KB1 RPS6KB1 12090 -0.027 0.22 NO
38 MTOR MTOR MTOR 12188 -0.028 0.22 NO
39 DDIT4 DDIT4 DDIT4 12375 -0.031 0.22 NO
40 EIF4E2 EIF4E2 EIF4E2 12668 -0.035 0.2 NO
41 CAB39 CAB39 CAB39 12799 -0.037 0.2 NO
42 PIK3R2 PIK3R2 PIK3R2 13432 -0.045 0.18 NO
43 HIF1A HIF1A HIF1A 13490 -0.046 0.18 NO
44 PIK3CB PIK3CB PIK3CB 14734 -0.066 0.12 NO
45 EIF4E EIF4E EIF4E 14750 -0.067 0.14 NO
46 ULK3 ULK3 ULK3 14873 -0.069 0.14 NO
47 RPS6KB2 RPS6KB2 RPS6KB2 15386 -0.08 0.12 NO
48 RPS6KA1 RPS6KA1 RPS6KA1 15658 -0.087 0.12 NO
49 EIF4EBP1 EIF4EBP1 EIF4EBP1 16737 -0.12 0.084 NO
50 VEGFA VEGFA VEGFA 17125 -0.15 0.086 NO

Figure S41.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PURINE METABOLISM.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG TYROSINE METABOLISM

Table S22.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AGTR1 AGTR1 AGTR1 100 0.8 0.22 YES
2 PRKCB PRKCB PRKCB 274 0.68 0.4 YES
3 MEF2C MEF2C MEF2C 1161 0.45 0.48 YES
4 AGT AGT AGT 1976 0.34 0.53 YES
5 MEF2A MEF2A MEF2A 4733 0.12 0.42 NO
6 MEF2D MEF2D MEF2D 4835 0.12 0.45 NO
7 PRKCA PRKCA PRKCA 5424 0.093 0.44 NO
8 JUN JUN JUN 6109 0.072 0.42 NO
9 GNAQ GNAQ GNAQ 6639 0.057 0.41 NO
10 ELK1 ELK1 ELK1 7066 0.048 0.4 NO
11 CALM3 CALM3 CALM3 7092 0.047 0.41 NO
12 ATF2 ATF2 ATF2 7412 0.041 0.41 NO
13 CALM1 CALM1 CALM1 7817 0.034 0.4 NO
14 SOS1 SOS1 SOS1 8071 0.029 0.39 NO
15 MAP3K1 MAP3K1 MAP3K1 9051 0.014 0.34 NO
16 GRB2 GRB2 GRB2 9073 0.014 0.34 NO
17 PTK2B PTK2B PTK2B 9139 0.013 0.34 NO
18 CALM2 CALM2 CALM2 9674 0.0049 0.32 NO
19 RAF1 RAF1 RAF1 10029 0.0001 0.3 NO
20 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.29 NO
21 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.28 NO
22 SHC1 SHC1 SHC1 10732 -0.01 0.27 NO
23 MAPK8 MAPK8 MAPK8 11387 -0.019 0.24 NO
24 MAP2K2 MAP2K2 MAP2K2 11498 -0.02 0.24 NO
25 MAP2K4 MAP2K4 MAP2K4 12946 -0.039 0.17 NO
26 MAP2K1 MAP2K1 MAP2K1 13417 -0.045 0.16 NO
27 RAC1 RAC1 RAC1 13625 -0.048 0.16 NO
28 PTK2 PTK2 PTK2 13919 -0.052 0.16 NO
29 SRC SRC SRC 13949 -0.053 0.17 NO
30 PAK1 PAK1 PAK1 14509 -0.062 0.16 NO
31 EGFR EGFR EGFR 16365 -0.11 0.091 NO
32 HRAS HRAS HRAS 16731 -0.12 0.11 NO

Figure S43.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TYROSINE METABOLISM.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TYROSINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG TRYPTOPHAN METABOLISM

Table S23.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADCY5 ADCY5 ADCY5 120 0.79 0.042 YES
2 PDE1A PDE1A PDE1A 127 0.78 0.091 YES
3 ADCY2 ADCY2 ADCY2 185 0.74 0.13 YES
4 PDE1B PDE1B PDE1B 198 0.73 0.18 YES
5 ADCYAP1 ADCYAP1 ADCYAP1 227 0.71 0.22 YES
6 ADCYAP1R1 ADCYAP1R1 ADCYAP1R1 336 0.65 0.26 YES
7 NTRK1 NTRK1 NTRK1 768 0.52 0.26 YES
8 PRKAR2B PRKAR2B PRKAR2B 879 0.5 0.29 YES
9 CAMK4 CAMK4 CAMK4 1069 0.47 0.31 YES
10 MEF2C MEF2C MEF2C 1161 0.45 0.33 YES
11 AKT3 AKT3 AKT3 1433 0.41 0.34 YES
12 NGF NGF NGF 1445 0.41 0.37 YES
13 ADORA2A ADORA2A ADORA2A 1569 0.39 0.39 YES
14 SHC2 SHC2 SHC2 1728 0.37 0.4 YES
15 ADCY4 ADCY4 ADCY4 1858 0.35 0.42 YES
16 SH3GL2 SH3GL2 SH3GL2 2369 0.29 0.41 YES
17 PRKCG PRKCG PRKCG 2408 0.29 0.42 YES
18 MAPK11 MAPK11 MAPK11 2806 0.25 0.42 YES
19 ADCY1 ADCY1 ADCY1 3032 0.23 0.42 YES
20 PRKACB PRKACB PRKACB 3079 0.23 0.43 YES
21 RPS6KA2 RPS6KA2 RPS6KA2 3385 0.2 0.42 YES
22 PIK3R1 PIK3R1 PIK3R1 3717 0.18 0.42 YES
23 ADCY9 ADCY9 ADCY9 3857 0.17 0.42 YES
24 NTRK2 NTRK2 NTRK2 3907 0.16 0.43 YES
25 IRS2 IRS2 IRS2 4015 0.16 0.43 YES
26 FOXO4 FOXO4 FOXO4 4021 0.16 0.44 YES
27 ITPR2 ITPR2 ITPR2 4023 0.16 0.45 YES
28 SHC3 SHC3 SHC3 4213 0.15 0.45 YES
29 FOXO1 FOXO1 FOXO1 4607 0.13 0.44 YES
30 DUSP3 DUSP3 DUSP3 4636 0.13 0.44 YES
31 DNM1 DNM1 DNM1 4646 0.13 0.45 YES
32 MEF2A MEF2A MEF2A 4733 0.12 0.46 YES
33 RAP1A RAP1A RAP1A 4751 0.12 0.46 YES
34 CDKN1B CDKN1B CDKN1B 5044 0.11 0.45 NO
35 IRS1 IRS1 IRS1 5411 0.094 0.44 NO
36 PRKCA PRKCA PRKCA 5424 0.093 0.44 NO
37 RAPGEF1 RAPGEF1 RAPGEF1 5624 0.087 0.44 NO
38 NR4A1 NR4A1 NR4A1 5640 0.087 0.44 NO
39 PRKCE PRKCE PRKCE 5652 0.086 0.45 NO
40 RPS6KA5 RPS6KA5 RPS6KA5 5674 0.086 0.45 NO
41 PTEN PTEN PTEN 5874 0.078 0.45 NO
42 PRKACA PRKACA PRKACA 5883 0.078 0.45 NO
43 DUSP4 DUSP4 DUSP4 6249 0.068 0.44 NO
44 MAPK12 MAPK12 MAPK12 6306 0.066 0.44 NO
45 MAP2K5 MAP2K5 MAP2K5 6586 0.059 0.42 NO
46 PLCG1 PLCG1 PLCG1 6668 0.057 0.42 NO
47 PRKAR2A PRKAR2A PRKAR2A 6694 0.056 0.43 NO
48 MAPKAP1 MAPKAP1 MAPKAP1 6743 0.054 0.43 NO
49 ELK1 ELK1 ELK1 7066 0.048 0.41 NO
50 CALM3 CALM3 CALM3 7092 0.047 0.42 NO
51 BAD BAD BAD 7494 0.04 0.4 NO
52 AKT2 AKT2 AKT2 7538 0.039 0.4 NO
53 STAT3 STAT3 STAT3 7573 0.038 0.4 NO
54 ADCY6 ADCY6 ADCY6 7627 0.037 0.4 NO
55 ADCY7 ADCY7 ADCY7 7678 0.036 0.4 NO
56 PRKAR1A PRKAR1A PRKAR1A 7769 0.035 0.39 NO
57 CALM1 CALM1 CALM1 7817 0.034 0.39 NO
58 AP2A2 AP2A2 AP2A2 7879 0.033 0.39 NO
59 KIDINS220 KIDINS220 KIDINS220 7918 0.032 0.39 NO
60 CASP9 CASP9 CASP9 7954 0.032 0.39 NO
61 CREB1 CREB1 CREB1 8057 0.03 0.39 NO
62 SOS1 SOS1 SOS1 8071 0.029 0.39 NO
63 RHOA RHOA RHOA 8123 0.028 0.39 NO
64 TSC2 TSC2 TSC2 8168 0.028 0.39 NO
65 PDPK1 PDPK1 PDPK1 8498 0.022 0.37 NO
66 RPS6KA3 RPS6KA3 RPS6KA3 8635 0.021 0.36 NO
67 PIK3CA PIK3CA PIK3CA 8702 0.02 0.36 NO
68 FOXO3 FOXO3 FOXO3 8799 0.018 0.36 NO
69 PRKACG PRKACG PRKACG 8877 0.017 0.36 NO
70 GRB2 GRB2 GRB2 9073 0.014 0.34 NO
71 ADCY8 ADCY8 ADCY8 9078 0.014 0.35 NO
72 FRS2 FRS2 FRS2 9246 0.011 0.34 NO
73 PRKAR1B PRKAR1B PRKAR1B 9259 0.011 0.34 NO
74 CALM2 CALM2 CALM2 9674 0.0049 0.32 NO
75 THEM4 THEM4 THEM4 9736 0.004 0.31 NO
76 BRAF BRAF BRAF 9777 0.0036 0.31 NO
77 MAPKAPK2 MAPKAPK2 MAPKAPK2 9787 0.0034 0.31 NO
78 AP2A1 AP2A1 AP2A1 9914 0.0015 0.3 NO
79 MDM2 MDM2 MDM2 9919 0.0014 0.3 NO
80 AP2B1 AP2B1 AP2B1 9982 0.0007 0.3 NO
81 RAF1 RAF1 RAF1 10029 0.0001 0.3 NO
82 AKT1S1 AKT1S1 AKT1S1 10089 -0.00061 0.3 NO
83 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.29 NO
84 RICTOR RICTOR RICTOR 10240 -0.0028 0.29 NO
85 PPP2CB PPP2CB PPP2CB 10303 -0.0037 0.28 NO
86 ADCY3 ADCY3 ADCY3 10333 -0.0041 0.28 NO
87 DUSP6 DUSP6 DUSP6 10362 -0.0046 0.28 NO
88 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.28 NO
89 MLST8 MLST8 MLST8 10365 -0.0046 0.28 NO
90 MAPK14 MAPK14 MAPK14 10441 -0.0058 0.28 NO
91 AKT1 AKT1 AKT1 10625 -0.0084 0.27 NO
92 DNAL4 DNAL4 DNAL4 10641 -0.0086 0.27 NO
93 ATF1 ATF1 ATF1 10643 -0.0086 0.27 NO
94 PPP2R1A PPP2R1A PPP2R1A 10647 -0.0088 0.27 NO
95 SHC1 SHC1 SHC1 10732 -0.01 0.27 NO
96 GSK3A GSK3A GSK3A 10942 -0.013 0.26 NO
97 MAPK7 MAPK7 MAPK7 11217 -0.016 0.24 NO
98 CRK CRK CRK 11285 -0.017 0.24 NO
99 MAPKAPK3 MAPKAPK3 MAPKAPK3 11370 -0.018 0.24 NO
100 AP2M1 AP2M1 AP2M1 11428 -0.019 0.23 NO
101 MAP2K2 MAP2K2 MAP2K2 11498 -0.02 0.23 NO
102 CLTA CLTA CLTA 12027 -0.026 0.2 NO
103 YWHAB YWHAB YWHAB 12084 -0.027 0.2 NO
104 MTOR MTOR MTOR 12188 -0.028 0.2 NO
105 RALGDS RALGDS RALGDS 12305 -0.03 0.2 NO
106 ADRBK1 ADRBK1 ADRBK1 12436 -0.032 0.19 NO
107 PPP2CA PPP2CA PPP2CA 12740 -0.036 0.18 NO
108 KRAS KRAS KRAS 12775 -0.037 0.18 NO
109 AP2S1 AP2S1 AP2S1 13055 -0.04 0.16 NO
110 CLTC CLTC CLTC 13252 -0.043 0.16 NO
111 RIT1 RIT1 RIT1 13262 -0.043 0.16 NO
112 MAP2K1 MAP2K1 MAP2K1 13417 -0.045 0.15 NO
113 PIK3R2 PIK3R2 PIK3R2 13432 -0.045 0.16 NO
114 PPP2R5D PPP2R5D PPP2R5D 13461 -0.046 0.16 NO
115 CHUK CHUK CHUK 13617 -0.048 0.15 NO
116 CDKN1A CDKN1A CDKN1A 13711 -0.049 0.15 NO
117 PRKCD PRKCD PRKCD 13877 -0.052 0.14 NO
118 SRC SRC SRC 13949 -0.053 0.14 NO
119 DNM2 DNM2 DNM2 14278 -0.059 0.13 NO
120 RALB RALB RALB 14571 -0.064 0.12 NO
121 PIK3CB PIK3CB PIK3CB 14734 -0.066 0.11 NO
122 NRAS NRAS NRAS 15221 -0.077 0.091 NO
123 PPP2R1B PPP2R1B PPP2R1B 15236 -0.077 0.095 NO
124 RPS6KB2 RPS6KB2 RPS6KB2 15386 -0.08 0.092 NO
125 RPS6KA1 RPS6KA1 RPS6KA1 15658 -0.087 0.083 NO
126 RALA RALA RALA 15663 -0.087 0.088 NO
127 PHLPP1 PHLPP1 PHLPP1 16059 -0.098 0.073 NO
128 HRAS HRAS HRAS 16731 -0.12 0.045 NO
129 DUSP7 DUSP7 DUSP7 17024 -0.14 0.038 NO
130 ITPR3 ITPR3 ITPR3 17147 -0.15 0.04 NO
131 MAPK13 MAPK13 MAPK13 17616 -0.19 0.027 NO
132 CDK1 CDK1 CDK1 18021 -0.24 0.02 NO
133 TRIB3 TRIB3 TRIB3 18330 -0.29 0.021 NO

Figure S45.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TRYPTOPHAN METABOLISM.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TRYPTOPHAN METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

Table S24.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SLC2A4 SLC2A4 SLC2A4 301 0.67 0.069 YES
2 ADIPOQ ADIPOQ ADIPOQ 395 0.63 0.14 YES
3 FABP4 FABP4 FABP4 606 0.56 0.2 YES
4 EBF1 EBF1 EBF1 738 0.53 0.26 YES
5 CD36 CD36 CD36 1274 0.44 0.29 YES
6 SMARCD3 SMARCD3 SMARCD3 1347 0.42 0.34 YES
7 PLIN1 PLIN1 PLIN1 1721 0.37 0.37 YES
8 LPL LPL LPL 1743 0.36 0.41 YES
9 EGR2 EGR2 EGR2 1833 0.35 0.45 YES
10 WNT1 WNT1 WNT1 2442 0.28 0.46 YES
11 NR2F2 NR2F2 NR2F2 2463 0.28 0.49 YES
12 LEP LEP LEP 3497 0.19 0.46 NO
13 TGFB1 TGFB1 TGFB1 4137 0.15 0.45 NO
14 TBL1X TBL1X TBL1X 4542 0.13 0.44 NO
15 PPARGC1A PPARGC1A PPARGC1A 4892 0.12 0.44 NO
16 CEBPD CEBPD CEBPD 5305 0.098 0.43 NO
17 WNT10B WNT10B WNT10B 5379 0.095 0.44 NO
18 MED7 MED7 MED7 5908 0.077 0.42 NO
19 NCOA1 NCOA1 NCOA1 6504 0.061 0.39 NO
20 CREBBP CREBBP CREBBP 6771 0.054 0.38 NO
21 MED29 MED29 MED29 6824 0.053 0.39 NO
22 MED13L MED13L MED13L 7041 0.048 0.38 NO
23 NCOR1 NCOR1 NCOR1 7603 0.038 0.36 NO
24 MED21 MED21 MED21 7736 0.035 0.36 NO
25 MED22 MED22 MED22 7970 0.031 0.35 NO
26 MED11 MED11 MED11 8166 0.028 0.34 NO
27 PPARG PPARG PPARG 8181 0.028 0.34 NO
28 NCOR2 NCOR2 NCOR2 8536 0.022 0.33 NO
29 CDK19 CDK19 CDK19 8775 0.018 0.32 NO
30 NCOA2 NCOA2 NCOA2 9108 0.013 0.3 NO
31 CCND3 CCND3 CCND3 9325 0.0099 0.29 NO
32 MED16 MED16 MED16 9365 0.0091 0.29 NO
33 MED12 MED12 MED12 9496 0.0074 0.28 NO
34 EP300 EP300 EP300 9664 0.0051 0.28 NO
35 ANGPTL4 ANGPTL4 ANGPTL4 9781 0.0035 0.27 NO
36 MED9 MED9 MED9 10109 -0.0008 0.25 NO
37 RELA RELA RELA 10208 -0.0024 0.25 NO
38 HDAC3 HDAC3 HDAC3 10224 -0.0026 0.25 NO
39 MED17 MED17 MED17 10276 -0.0033 0.24 NO
40 MED1 MED1 MED1 10344 -0.0042 0.24 NO
41 MED18 MED18 MED18 10381 -0.0048 0.24 NO
42 PCK1 PCK1 PCK1 10384 -0.0049 0.24 NO
43 CDK8 CDK8 CDK8 10563 -0.0076 0.23 NO
44 NCOA3 NCOA3 NCOA3 10640 -0.0086 0.23 NO
45 MED26 MED26 MED26 10692 -0.0094 0.23 NO
46 PPARA PPARA PPARA 10756 -0.01 0.22 NO
47 CEBPB CEBPB CEBPB 10874 -0.012 0.22 NO
48 RXRA RXRA RXRA 11601 -0.021 0.18 NO
49 MED31 MED31 MED31 11870 -0.024 0.17 NO
50 MED19 MED19 MED19 11890 -0.025 0.18 NO
51 MED25 MED25 MED25 12017 -0.026 0.17 NO
52 MED23 MED23 MED23 12058 -0.027 0.17 NO
53 MED4 MED4 MED4 12148 -0.028 0.17 NO
54 MED8 MED8 MED8 12344 -0.031 0.16 NO
55 MED6 MED6 MED6 12406 -0.031 0.17 NO
56 MED10 MED10 MED10 12539 -0.034 0.16 NO
57 MED15 MED15 MED15 12663 -0.035 0.16 NO
58 CDK4 CDK4 CDK4 13038 -0.04 0.15 NO
59 NCOA6 NCOA6 NCOA6 13338 -0.044 0.14 NO
60 TNF TNF TNF 13563 -0.047 0.13 NO
61 PRIC285 PRIC285 PRIC285 14221 -0.058 0.1 NO
62 TGS1 TGS1 TGS1 14603 -0.064 0.089 NO
63 MED14 MED14 MED14 14699 -0.066 0.092 NO
64 MED27 MED27 MED27 14878 -0.07 0.092 NO
65 TBL1XR1 TBL1XR1 TBL1XR1 15622 -0.086 0.063 NO
66 CCNC CCNC CCNC 15773 -0.09 0.066 NO
67 MED30 MED30 MED30 15849 -0.092 0.074 NO
68 MED24 MED24 MED24 15952 -0.095 0.081 NO
69 MED20 MED20 MED20 16080 -0.099 0.086 NO
70 SREBF1 SREBF1 SREBF1 16689 -0.12 0.069 NO
71 KLF4 KLF4 KLF4 16717 -0.12 0.084 NO
72 KLF5 KLF5 KLF5 17638 -0.19 0.058 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ABC TRANSPORTERS

Table S25.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 274 0.68 0.056 YES
2 KLRG1 KLRG1 KLRG1 350 0.64 0.12 YES
3 FCGR2B FCGR2B FCGR2B 560 0.57 0.17 YES
4 BTK BTK BTK 632 0.55 0.22 YES
5 ITK ITK ITK 873 0.5 0.26 YES
6 MS4A2 MS4A2 MS4A2 915 0.5 0.31 YES
7 FCER1A FCER1A FCER1A 1230 0.44 0.34 YES
8 S1PR1 S1PR1 S1PR1 1365 0.42 0.38 YES
9 VAV1 VAV1 VAV1 1557 0.39 0.41 YES
10 LAT2 LAT2 LAT2 1741 0.36 0.44 YES
11 WIPF1 WIPF1 WIPF1 2015 0.33 0.46 YES
12 HCLS1 HCLS1 HCLS1 2039 0.33 0.49 YES
13 NFATC2 NFATC2 NFATC2 2305 0.3 0.5 YES
14 PPAP2A PPAP2A PPAP2A 2330 0.3 0.54 YES
15 LAT LAT LAT 2393 0.29 0.56 YES
16 LCP2 LCP2 LCP2 2616 0.27 0.58 YES
17 FYN FYN FYN 2794 0.25 0.59 YES
18 FCER1G FCER1G FCER1G 2839 0.25 0.62 YES
19 INPP5D INPP5D INPP5D 3030 0.23 0.63 YES
20 GAB2 GAB2 GAB2 3264 0.21 0.64 YES
21 PIK3R1 PIK3R1 PIK3R1 3717 0.18 0.64 YES
22 DOK1 DOK1 DOK1 4138 0.15 0.63 YES
23 FER FER FER 4142 0.15 0.64 YES
24 DUSP1 DUSP1 DUSP1 4165 0.15 0.66 YES
25 PLA2G1B PLA2G1B PLA2G1B 5859 0.079 0.58 NO
26 PTPN13 PTPN13 PTPN13 6081 0.073 0.57 NO
27 JUN JUN JUN 6109 0.072 0.58 NO
28 PLCG1 PLCG1 PLCG1 6668 0.057 0.55 NO
29 CBL CBL CBL 6944 0.05 0.55 NO
30 MAP2K7 MAP2K7 MAP2K7 7147 0.046 0.54 NO
31 SOS1 SOS1 SOS1 8071 0.029 0.49 NO
32 CBLB CBLB CBLB 8430 0.024 0.48 NO
33 SYK SYK SYK 8660 0.02 0.46 NO
34 PIK3CA PIK3CA PIK3CA 8702 0.02 0.46 NO
35 PTPN11 PTPN11 PTPN11 8792 0.018 0.46 NO
36 RASA1 RASA1 RASA1 8891 0.016 0.46 NO
37 NFKB1 NFKB1 NFKB1 8897 0.016 0.46 NO
38 MAP3K1 MAP3K1 MAP3K1 9051 0.014 0.45 NO
39 GRB2 GRB2 GRB2 9073 0.014 0.45 NO
40 LYN LYN LYN 9166 0.012 0.45 NO
41 RAF1 RAF1 RAF1 10029 0.0001 0.4 NO
42 RELA RELA RELA 10208 -0.0024 0.4 NO
43 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.39 NO
44 SPHK1 SPHK1 SPHK1 10343 -0.0042 0.39 NO
45 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.39 NO
46 PLA2G4A PLA2G4A PLA2G4A 10507 -0.0069 0.38 NO
47 AKT1 AKT1 AKT1 10625 -0.0084 0.38 NO
48 SHC1 SHC1 SHC1 10732 -0.01 0.37 NO
49 IKBKB IKBKB IKBKB 10734 -0.01 0.37 NO
50 FOS FOS FOS 10860 -0.012 0.37 NO
51 MAPK8 MAPK8 MAPK8 11387 -0.019 0.34 NO
52 MAP2K2 MAP2K2 MAP2K2 11498 -0.02 0.34 NO
53 PXN PXN PXN 11881 -0.025 0.32 NO
54 MAP2K4 MAP2K4 MAP2K4 12946 -0.039 0.26 NO
55 IKBKG IKBKG IKBKG 13017 -0.04 0.27 NO
56 PAK2 PAK2 PAK2 13400 -0.045 0.25 NO
57 MAP2K1 MAP2K1 MAP2K1 13417 -0.045 0.25 NO
58 CHUK CHUK CHUK 13617 -0.048 0.25 NO
59 PTK2 PTK2 PTK2 13919 -0.052 0.24 NO
60 PLD2 PLD2 PLD2 14728 -0.066 0.2 NO
61 HRAS HRAS HRAS 16731 -0.12 0.11 NO

Figure S49.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ABC TRANSPORTERS.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG MAPK SIGNALING PATHWAY

Table S26.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADCY5 ADCY5 ADCY5 120 0.79 0.026 YES
2 PDE1A PDE1A PDE1A 127 0.78 0.058 YES
3 ADCY2 ADCY2 ADCY2 185 0.74 0.085 YES
4 PDE1B PDE1B PDE1B 198 0.73 0.12 YES
5 ADCYAP1 ADCYAP1 ADCYAP1 227 0.71 0.14 YES
6 ADCYAP1R1 ADCYAP1R1 ADCYAP1R1 336 0.65 0.16 YES
7 NGFR NGFR NGFR 491 0.59 0.18 YES
8 NTRK1 NTRK1 NTRK1 768 0.52 0.19 YES
9 PRKAR2B PRKAR2B PRKAR2B 879 0.5 0.2 YES
10 CAMK4 CAMK4 CAMK4 1069 0.47 0.21 YES
11 MEF2C MEF2C MEF2C 1161 0.45 0.22 YES
12 ARHGEF6 ARHGEF6 ARHGEF6 1326 0.43 0.23 YES
13 FGD2 FGD2 FGD2 1371 0.42 0.25 YES
14 AKT3 AKT3 AKT3 1433 0.41 0.26 YES
15 NGF NGF NGF 1445 0.41 0.28 YES
16 RASGRF2 RASGRF2 RASGRF2 1520 0.4 0.29 YES
17 VAV1 VAV1 VAV1 1557 0.39 0.3 YES
18 ADORA2A ADORA2A ADORA2A 1569 0.39 0.32 YES
19 SORCS3 SORCS3 SORCS3 1705 0.37 0.33 YES
20 SHC2 SHC2 SHC2 1728 0.37 0.34 YES
21 ADCY4 ADCY4 ADCY4 1858 0.35 0.35 YES
22 MAG MAG MAG 2301 0.3 0.34 YES
23 SH3GL2 SH3GL2 SH3GL2 2369 0.29 0.34 YES
24 PRKCG PRKCG PRKCG 2408 0.29 0.36 YES
25 FGD3 FGD3 FGD3 2526 0.28 0.36 YES
26 PREX1 PREX1 PREX1 2707 0.26 0.36 YES
27 MAPK11 MAPK11 MAPK11 2806 0.25 0.37 YES
28 ARHGEF17 ARHGEF17 ARHGEF17 2898 0.24 0.37 YES
29 ADCY1 ADCY1 ADCY1 3032 0.23 0.37 YES
30 PRKACB PRKACB PRKACB 3079 0.23 0.38 YES
31 RPS6KA2 RPS6KA2 RPS6KA2 3385 0.2 0.37 YES
32 ARHGEF9 ARHGEF9 ARHGEF9 3407 0.2 0.38 YES
33 MCF2 MCF2 MCF2 3537 0.19 0.38 YES
34 PIK3R1 PIK3R1 PIK3R1 3717 0.18 0.38 YES
35 NGFRAP1 NGFRAP1 NGFRAP1 3722 0.18 0.38 YES
36 APH1B APH1B APH1B 3856 0.17 0.38 YES
37 ADCY9 ADCY9 ADCY9 3857 0.17 0.39 YES
38 NTRK2 NTRK2 NTRK2 3907 0.16 0.4 YES
39 RASGRF1 RASGRF1 RASGRF1 3962 0.16 0.4 YES
40 IRS2 IRS2 IRS2 4015 0.16 0.4 YES
41 ARHGAP4 ARHGAP4 ARHGAP4 4016 0.16 0.41 YES
42 FOXO4 FOXO4 FOXO4 4021 0.16 0.42 YES
43 ITPR2 ITPR2 ITPR2 4023 0.16 0.42 YES
44 SHC3 SHC3 SHC3 4213 0.15 0.42 YES
45 FGD1 FGD1 FGD1 4303 0.14 0.42 YES
46 FOXO1 FOXO1 FOXO1 4607 0.13 0.41 YES
47 DUSP3 DUSP3 DUSP3 4636 0.13 0.41 YES
48 DNM1 DNM1 DNM1 4646 0.13 0.42 YES
49 KALRN KALRN KALRN 4722 0.12 0.42 YES
50 MEF2A MEF2A MEF2A 4733 0.12 0.42 YES
51 RAP1A RAP1A RAP1A 4751 0.12 0.43 YES
52 CDKN1B CDKN1B CDKN1B 5044 0.11 0.42 NO
53 ITSN1 ITSN1 ITSN1 5163 0.1 0.41 NO
54 PLEKHG2 PLEKHG2 PLEKHG2 5361 0.096 0.41 NO
55 IRS1 IRS1 IRS1 5411 0.094 0.41 NO
56 PRKCA PRKCA PRKCA 5424 0.093 0.41 NO
57 ARHGEF3 ARHGEF3 ARHGEF3 5431 0.093 0.41 NO
58 RAPGEF1 RAPGEF1 RAPGEF1 5624 0.087 0.41 NO
59 NR4A1 NR4A1 NR4A1 5640 0.087 0.41 NO
60 PRKCE PRKCE PRKCE 5652 0.086 0.41 NO
61 RPS6KA5 RPS6KA5 RPS6KA5 5674 0.086 0.42 NO
62 PTEN PTEN PTEN 5874 0.078 0.41 NO
63 PRKACA PRKACA PRKACA 5883 0.078 0.41 NO
64 LINGO1 LINGO1 LINGO1 5904 0.078 0.41 NO
65 TIAM1 TIAM1 TIAM1 6104 0.072 0.4 NO
66 DUSP4 DUSP4 DUSP4 6249 0.068 0.4 NO
67 MAPK12 MAPK12 MAPK12 6306 0.066 0.4 NO
68 ARHGEF2 ARHGEF2 ARHGEF2 6317 0.066 0.4 NO
69 MAP2K5 MAP2K5 MAP2K5 6586 0.059 0.39 NO
70 TRAF6 TRAF6 TRAF6 6613 0.058 0.39 NO
71 PLCG1 PLCG1 PLCG1 6668 0.057 0.39 NO
72 PRKAR2A PRKAR2A PRKAR2A 6694 0.056 0.39 NO
73 MAPKAP1 MAPKAP1 MAPKAP1 6743 0.054 0.39 NO
74 TRIO TRIO TRIO 6750 0.054 0.39 NO
75 ELK1 ELK1 ELK1 7066 0.048 0.38 NO
76 CALM3 CALM3 CALM3 7092 0.047 0.38 NO
77 BAD BAD BAD 7494 0.04 0.36 NO
78 PSEN2 PSEN2 PSEN2 7498 0.04 0.36 NO
79 AKAP13 AKAP13 AKAP13 7509 0.04 0.36 NO
80 AKT2 AKT2 AKT2 7538 0.039 0.36 NO
81 STAT3 STAT3 STAT3 7573 0.038 0.36 NO
82 ADCY6 ADCY6 ADCY6 7627 0.037 0.36 NO
83 ADCY7 ADCY7 ADCY7 7678 0.036 0.36 NO
84 ARHGEF18 ARHGEF18 ARHGEF18 7698 0.036 0.36 NO
85 NFKBIA NFKBIA NFKBIA 7718 0.036 0.36 NO
86 PRKAR1A PRKAR1A PRKAR1A 7769 0.035 0.36 NO
87 CALM1 CALM1 CALM1 7817 0.034 0.36 NO
88 AP2A2 AP2A2 AP2A2 7879 0.033 0.36 NO
89 KIDINS220 KIDINS220 KIDINS220 7918 0.032 0.35 NO
90 MAGED1 MAGED1 MAGED1 7942 0.032 0.35 NO
91 CASP9 CASP9 CASP9 7954 0.032 0.36 NO
92 CREB1 CREB1 CREB1 8057 0.03 0.35 NO
93 SOS1 SOS1 SOS1 8071 0.029 0.35 NO
94 RHOA RHOA RHOA 8123 0.028 0.35 NO
95 TSC2 TSC2 TSC2 8168 0.028 0.35 NO
96 RTN4 RTN4 RTN4 8190 0.027 0.35 NO
97 UBA52 UBA52 UBA52 8251 0.027 0.35 NO
98 ARHGEF1 ARHGEF1 ARHGEF1 8266 0.026 0.35 NO
99 PDPK1 PDPK1 PDPK1 8498 0.022 0.34 NO
100 RPS6KA3 RPS6KA3 RPS6KA3 8635 0.021 0.33 NO
101 PSENEN PSENEN PSENEN 8700 0.02 0.32 NO
102 PIK3CA PIK3CA PIK3CA 8702 0.02 0.33 NO
103 PCSK5 PCSK5 PCSK5 8764 0.018 0.32 NO
104 BCL2L11 BCL2L11 BCL2L11 8779 0.018 0.32 NO
105 FOXO3 FOXO3 FOXO3 8799 0.018 0.32 NO
106 PRKACG PRKACG PRKACG 8877 0.017 0.32 NO
107 GRB2 GRB2 GRB2 9073 0.014 0.31 NO
108 ADCY8 ADCY8 ADCY8 9078 0.014 0.31 NO
109 SQSTM1 SQSTM1 SQSTM1 9099 0.013 0.31 NO
110 SOS2 SOS2 SOS2 9149 0.012 0.31 NO
111 FRS2 FRS2 FRS2 9246 0.011 0.3 NO
112 PRKAR1B PRKAR1B PRKAR1B 9259 0.011 0.3 NO
113 FGD4 FGD4 FGD4 9310 0.01 0.3 NO
114 ARHGEF12 ARHGEF12 ARHGEF12 9326 0.0099 0.3 NO
115 RPS27A RPS27A RPS27A 9528 0.0069 0.29 NO
116 CALM2 CALM2 CALM2 9674 0.0049 0.28 NO
117 THEM4 THEM4 THEM4 9736 0.004 0.28 NO
118 BRAF BRAF BRAF 9777 0.0036 0.28 NO
119 MAPKAPK2 MAPKAPK2 MAPKAPK2 9787 0.0034 0.28 NO
120 AP2A1 AP2A1 AP2A1 9914 0.0015 0.27 NO
121 MDM2 MDM2 MDM2 9919 0.0014 0.27 NO
122 TIAM2 TIAM2 TIAM2 9977 0.00078 0.27 NO
123 AP2B1 AP2B1 AP2B1 9982 0.0007 0.27 NO
124 MYD88 MYD88 MYD88 9989 0.00057 0.27 NO
125 RAF1 RAF1 RAF1 10029 0.0001 0.26 NO
126 AKT1S1 AKT1S1 AKT1S1 10089 -0.00061 0.26 NO
127 ABR ABR ABR 10184 -0.002 0.26 NO
128 RELA RELA RELA 10208 -0.0024 0.25 NO
129 HDAC3 HDAC3 HDAC3 10224 -0.0026 0.25 NO
130 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.25 NO
131 RICTOR RICTOR RICTOR 10240 -0.0028 0.25 NO
132 PPP2CB PPP2CB PPP2CB 10303 -0.0037 0.25 NO
133 ADCY3 ADCY3 ADCY3 10333 -0.0041 0.25 NO
134 DUSP6 DUSP6 DUSP6 10362 -0.0046 0.25 NO
135 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.25 NO
136 MLST8 MLST8 MLST8 10365 -0.0046 0.25 NO
137 MAPK14 MAPK14 MAPK14 10441 -0.0058 0.24 NO
138 APH1A APH1A APH1A 10542 -0.0073 0.24 NO
139 AKT1 AKT1 AKT1 10625 -0.0084 0.24 NO
140 DNAL4 DNAL4 DNAL4 10641 -0.0086 0.23 NO
141 ATF1 ATF1 ATF1 10643 -0.0086 0.23 NO
142 PPP2R1A PPP2R1A PPP2R1A 10647 -0.0088 0.24 NO
143 SHC1 SHC1 SHC1 10732 -0.01 0.23 NO
144 IKBKB IKBKB IKBKB 10734 -0.01 0.23 NO
145 GSK3A GSK3A GSK3A 10942 -0.013 0.22 NO
146 MAPK7 MAPK7 MAPK7 11217 -0.016 0.21 NO
147 CRK CRK CRK 11285 -0.017 0.2 NO
148 CASP2 CASP2 CASP2 11346 -0.018 0.2 NO
149 MAPKAPK3 MAPKAPK3 MAPKAPK3 11370 -0.018 0.2 NO
150 MAPK8 MAPK8 MAPK8 11387 -0.019 0.2 NO
151 RIPK2 RIPK2 RIPK2 11403 -0.019 0.2 NO
152 AP2M1 AP2M1 AP2M1 11428 -0.019 0.2 NO
153 MAP2K2 MAP2K2 MAP2K2 11498 -0.02 0.2 NO
154 ARHGEF11 ARHGEF11 ARHGEF11 11746 -0.023 0.18 NO
155 ARHGDIA ARHGDIA ARHGDIA 11794 -0.024 0.18 NO
156 CLTA CLTA CLTA 12027 -0.026 0.17 NO
157 YWHAB YWHAB YWHAB 12084 -0.027 0.17 NO
158 MTOR MTOR MTOR 12188 -0.028 0.16 NO
159 RALGDS RALGDS RALGDS 12305 -0.03 0.16 NO
160 ADRBK1 ADRBK1 ADRBK1 12436 -0.032 0.15 NO
161 NCSTN NCSTN NCSTN 12549 -0.034 0.15 NO
162 PPP2CA PPP2CA PPP2CA 12740 -0.036 0.14 NO
163 KRAS KRAS KRAS 12775 -0.037 0.14 NO
164 PRDM4 PRDM4 PRDM4 12817 -0.037 0.14 NO
165 AP2S1 AP2S1 AP2S1 13055 -0.04 0.13 NO
166 AATF AATF AATF 13183 -0.042 0.12 NO
167 CLTC CLTC CLTC 13252 -0.043 0.12 NO
168 RIT1 RIT1 RIT1 13262 -0.043 0.12 NO
169 MAP2K1 MAP2K1 MAP2K1 13417 -0.045 0.12 NO
170 PIK3R2 PIK3R2 PIK3R2 13432 -0.045 0.12 NO
171 OMG OMG OMG 13440 -0.045 0.12 NO
172 PPP2R5D PPP2R5D PPP2R5D 13461 -0.046 0.12 NO
173 CHUK CHUK CHUK 13617 -0.048 0.11 NO
174 RAC1 RAC1 RAC1 13625 -0.048 0.12 NO
175 FURIN FURIN FURIN 13691 -0.049 0.11 NO
176 CDKN1A CDKN1A CDKN1A 13711 -0.049 0.12 NO
177 PSEN1 PSEN1 PSEN1 13859 -0.052 0.11 NO
178 PRKCD PRKCD PRKCD 13877 -0.052 0.11 NO
179 SRC SRC SRC 13949 -0.053 0.11 NO
180 OBSCN OBSCN OBSCN 14122 -0.056 0.1 NO
181 DNM2 DNM2 DNM2 14278 -0.059 0.095 NO
182 HDAC1 HDAC1 HDAC1 14330 -0.06 0.095 NO
183 ITGB3BP ITGB3BP ITGB3BP 14443 -0.062 0.092 NO
184 ARHGEF4 ARHGEF4 ARHGEF4 14553 -0.063 0.088 NO
185 RALB RALB RALB 14571 -0.064 0.09 NO
186 PIK3CB PIK3CB PIK3CB 14734 -0.066 0.084 NO
187 HDAC2 HDAC2 HDAC2 14742 -0.067 0.086 NO
188 YWHAE YWHAE YWHAE 15025 -0.072 0.074 NO
189 PRKCI PRKCI PRKCI 15079 -0.074 0.074 NO
190 SMPD2 SMPD2 SMPD2 15200 -0.076 0.071 NO
191 NRAS NRAS NRAS 15221 -0.077 0.073 NO
192 PPP2R1B PPP2R1B PPP2R1B 15236 -0.077 0.075 NO
193 IRAK1 IRAK1 IRAK1 15257 -0.077 0.077 NO
194 RPS6KB2 RPS6KB2 RPS6KB2 15386 -0.08 0.074 NO
195 NET1 NET1 NET1 15515 -0.083 0.07 NO
196 RPS6KA1 RPS6KA1 RPS6KA1 15658 -0.087 0.066 NO
197 RALA RALA RALA 15663 -0.087 0.07 NO
198 PCSK6 PCSK6 PCSK6 15812 -0.091 0.065 NO
199 CASP3 CASP3 CASP3 15877 -0.093 0.066 NO
200 ADAM17 ADAM17 ADAM17 16003 -0.096 0.063 NO
201 PHLPP1 PHLPP1 PHLPP1 16059 -0.098 0.064 NO
202 VAV3 VAV3 VAV3 16540 -0.12 0.043 NO
203 HRAS HRAS HRAS 16731 -0.12 0.038 NO
204 DUSP7 DUSP7 DUSP7 17024 -0.14 0.028 NO
205 ITPR3 ITPR3 ITPR3 17147 -0.15 0.027 NO
206 ECT2 ECT2 ECT2 17541 -0.18 0.013 NO
207 MAPK13 MAPK13 MAPK13 17616 -0.19 0.017 NO
208 CDK1 CDK1 CDK1 18021 -0.24 0.0049 NO
209 ARHGEF16 ARHGEF16 ARHGEF16 18076 -0.25 0.012 NO
210 NGEF NGEF NGEF 18157 -0.26 0.018 NO
211 TRIB3 TRIB3 TRIB3 18330 -0.29 0.021 NO

Figure S51.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG MAPK SIGNALING PATHWAY.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MAPK SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ERBB SIGNALING PATHWAY

Table S27.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AGTR1 AGTR1 AGTR1 100 0.8 0.11 YES
2 FGF2 FGF2 FGF2 384 0.63 0.19 YES
3 BMX BMX BMX 753 0.52 0.24 YES
4 TEK TEK TEK 1061 0.47 0.29 YES
5 DOK2 DOK2 DOK2 1299 0.43 0.34 YES
6 ANGPT1 ANGPT1 ANGPT1 1351 0.42 0.4 YES
7 FES FES FES 2697 0.26 0.37 YES
8 FYN FYN FYN 2794 0.25 0.4 YES
9 ANGPT4 ANGPT4 ANGPT4 3185 0.22 0.41 YES
10 NOS3 NOS3 NOS3 3196 0.22 0.44 YES
11 MMP2 MMP2 MMP2 3229 0.21 0.47 YES
12 FN1 FN1 FN1 3255 0.21 0.5 YES
13 ETS1 ETS1 ETS1 3325 0.2 0.52 YES
14 STAT5A STAT5A STAT5A 3465 0.19 0.55 YES
15 ITGA5 ITGA5 ITGA5 3551 0.19 0.57 YES
16 PIK3R1 PIK3R1 PIK3R1 3717 0.18 0.58 YES
17 STAT5B STAT5B STAT5B 4120 0.15 0.58 YES
18 FOXO1 FOXO1 FOXO1 4607 0.13 0.58 NO
19 ITGB1 ITGB1 ITGB1 6227 0.069 0.5 NO
20 ELF2 ELF2 ELF2 6889 0.052 0.47 NO
21 ELK1 ELK1 ELK1 7066 0.048 0.47 NO
22 GRB14 GRB14 GRB14 8421 0.024 0.4 NO
23 PIK3CA PIK3CA PIK3CA 8702 0.02 0.39 NO
24 PTPN11 PTPN11 PTPN11 8792 0.018 0.39 NO
25 RASA1 RASA1 RASA1 8891 0.016 0.38 NO
26 NFKB1 NFKB1 NFKB1 8897 0.016 0.39 NO
27 GRB2 GRB2 GRB2 9073 0.014 0.38 NO
28 NCK1 NCK1 NCK1 9691 0.0047 0.35 NO
29 RELA RELA RELA 10208 -0.0024 0.32 NO
30 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.32 NO
31 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.31 NO
32 MAPK14 MAPK14 MAPK14 10441 -0.0058 0.31 NO
33 AKT1 AKT1 AKT1 10625 -0.0084 0.3 NO
34 SHC1 SHC1 SHC1 10732 -0.01 0.3 NO
35 ELF1 ELF1 ELF1 11069 -0.015 0.28 NO
36 CRK CRK CRK 11285 -0.017 0.27 NO
37 MAPK8 MAPK8 MAPK8 11387 -0.019 0.27 NO
38 TNIP2 TNIP2 TNIP2 11625 -0.021 0.26 NO
39 PXN PXN PXN 11881 -0.025 0.25 NO
40 RPS6KB1 RPS6KB1 RPS6KB1 12090 -0.027 0.24 NO
41 ANGPT2 ANGPT2 ANGPT2 12705 -0.036 0.21 NO
42 TNF TNF TNF 13563 -0.047 0.17 NO
43 RAC1 RAC1 RAC1 13625 -0.048 0.18 NO
44 CDKN1A CDKN1A CDKN1A 13711 -0.049 0.18 NO
45 PTK2 PTK2 PTK2 13919 -0.052 0.18 NO
46 PAK1 PAK1 PAK1 14509 -0.062 0.15 NO
47 PLD2 PLD2 PLD2 14728 -0.066 0.15 NO
48 F2 F2 F2 16356 -0.11 0.081 NO
49 GRB7 GRB7 GRB7 18429 -0.32 0.016 NO

Figure S53.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ERBB SIGNALING PATHWAY.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ERBB SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CALCIUM SIGNALING PATHWAY

Table S28.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HAND2 HAND2 HAND2 7 0.98 0.11 YES
2 IGF1 IGF1 IGF1 84 0.82 0.2 YES
3 FGF2 FGF2 FGF2 384 0.63 0.25 YES
4 PRKAR2B PRKAR2B PRKAR2B 879 0.5 0.28 YES
5 PIK3CG PIK3CG PIK3CG 947 0.49 0.34 YES
6 CAMK4 CAMK4 CAMK4 1069 0.47 0.38 YES
7 MEF2C MEF2C MEF2C 1161 0.45 0.43 YES
8 NFATC4 NFATC4 NFATC4 1668 0.38 0.44 YES
9 ACTA1 ACTA1 ACTA1 1883 0.35 0.47 YES
10 CTF1 CTF1 CTF1 1968 0.34 0.5 YES
11 AGT AGT AGT 1976 0.34 0.54 YES
12 CAMK1G CAMK1G CAMK1G 2090 0.32 0.57 YES
13 NFATC2 NFATC2 NFATC2 2305 0.3 0.59 YES
14 CAMK1 CAMK1 CAMK1 2514 0.28 0.62 YES
15 NFATC1 NFATC1 NFATC1 3062 0.23 0.61 YES
16 PRKACB PRKACB PRKACB 3079 0.23 0.64 YES
17 PIK3R1 PIK3R1 PIK3R1 3717 0.18 0.62 YES
18 GATA4 GATA4 GATA4 3960 0.16 0.63 YES
19 PPP3CC PPP3CC PPP3CC 3981 0.16 0.64 YES
20 EDN1 EDN1 EDN1 4366 0.14 0.64 NO
21 PPP3CB PPP3CB PPP3CB 5187 0.1 0.61 NO
22 NKX2-5 NKX2-5 NKX2-5 6407 0.063 0.55 NO
23 PRKAR2A PRKAR2A PRKAR2A 6694 0.056 0.54 NO
24 HAND1 HAND1 HAND1 6759 0.054 0.54 NO
25 CREBBP CREBBP CREBBP 6771 0.054 0.55 NO
26 CALM3 CALM3 CALM3 7092 0.047 0.54 NO
27 NFATC3 NFATC3 NFATC3 7505 0.04 0.52 NO
28 PRKAR1A PRKAR1A PRKAR1A 7769 0.035 0.51 NO
29 CALM1 CALM1 CALM1 7817 0.034 0.51 NO
30 PPP3CA PPP3CA PPP3CA 8232 0.027 0.49 NO
31 PIK3CA PIK3CA PIK3CA 8702 0.02 0.47 NO
32 PRKACG PRKACG PRKACG 8877 0.017 0.46 NO
33 PRKAR1B PRKAR1B PRKAR1B 9259 0.011 0.44 NO
34 CALM2 CALM2 CALM2 9674 0.0049 0.42 NO
35 LIF LIF LIF 9967 0.00088 0.4 NO
36 RAF1 RAF1 RAF1 10029 0.0001 0.4 NO
37 FKBP1A FKBP1A FKBP1A 10214 -0.0024 0.39 NO
38 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.39 NO
39 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.38 NO
40 MAPK14 MAPK14 MAPK14 10441 -0.0058 0.38 NO
41 AKT1 AKT1 AKT1 10625 -0.0084 0.37 NO
42 MAPK8 MAPK8 MAPK8 11387 -0.019 0.33 NO
43 NPPA NPPA NPPA 11706 -0.022 0.32 NO
44 RPS6KB1 RPS6KB1 RPS6KB1 12090 -0.027 0.3 NO
45 CALR CALR CALR 12222 -0.029 0.3 NO
46 CSNK1A1 CSNK1A1 CSNK1A1 12780 -0.037 0.27 NO
47 MAP2K1 MAP2K1 MAP2K1 13417 -0.045 0.24 NO
48 GSK3B GSK3B GSK3B 13858 -0.052 0.22 NO
49 HBEGF HBEGF HBEGF 15511 -0.083 0.15 NO
50 F2 F2 F2 16356 -0.11 0.11 NO
51 HRAS HRAS HRAS 16731 -0.12 0.11 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CALCIUM SIGNALING PATHWAY.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CALCIUM SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

Table S29.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FGF10 FGF10 FGF10 52 0.86 0.049 YES
2 ADCY5 ADCY5 ADCY5 120 0.79 0.093 YES
3 PDE1A PDE1A PDE1A 127 0.78 0.14 YES
4 FGF7 FGF7 FGF7 179 0.74 0.18 YES
5 ADCY2 ADCY2 ADCY2 185 0.74 0.23 YES
6 PDE1B PDE1B PDE1B 198 0.73 0.27 YES
7 FGF2 FGF2 FGF2 384 0.63 0.3 YES
8 KL KL KL 603 0.56 0.32 YES
9 PRKAR2B PRKAR2B PRKAR2B 879 0.5 0.34 YES
10 CAMK4 CAMK4 CAMK4 1069 0.47 0.36 YES
11 FGFR1 FGFR1 FGFR1 1321 0.43 0.37 YES
12 FGF5 FGF5 FGF5 1396 0.42 0.39 YES
13 AKT3 AKT3 AKT3 1433 0.41 0.41 YES
14 FGF18 FGF18 FGF18 1561 0.39 0.43 YES
15 ADCY4 ADCY4 ADCY4 1858 0.35 0.44 YES
16 IL17RD IL17RD IL17RD 2239 0.3 0.43 YES
17 PRKCG PRKCG PRKCG 2408 0.29 0.44 YES
18 FGF1 FGF1 FGF1 2553 0.27 0.45 YES
19 FGF9 FGF9 FGF9 2629 0.26 0.46 YES
20 ADCY1 ADCY1 ADCY1 3032 0.23 0.45 YES
21 PRKACB PRKACB PRKACB 3079 0.23 0.46 YES
22 GAB2 GAB2 GAB2 3264 0.21 0.47 YES
23 STAT5A STAT5A STAT5A 3465 0.19 0.47 YES
24 PIK3R1 PIK3R1 PIK3R1 3717 0.18 0.47 YES
25 ADCY9 ADCY9 ADCY9 3857 0.17 0.47 YES
26 FOXO4 FOXO4 FOXO4 4021 0.16 0.47 YES
27 ITPR2 ITPR2 ITPR2 4023 0.16 0.48 YES
28 STAT5B STAT5B STAT5B 4120 0.15 0.48 YES
29 FOXO1 FOXO1 FOXO1 4607 0.13 0.47 NO
30 FGF20 FGF20 FGF20 4726 0.12 0.47 NO
31 CDKN1B CDKN1B CDKN1B 5044 0.11 0.46 NO
32 GAB1 GAB1 GAB1 5246 0.1 0.45 NO
33 FGFR2 FGFR2 FGFR2 5416 0.094 0.45 NO
34 PRKCA PRKCA PRKCA 5424 0.093 0.45 NO
35 NR4A1 NR4A1 NR4A1 5640 0.087 0.45 NO
36 PRKCE PRKCE PRKCE 5652 0.086 0.45 NO
37 PTEN PTEN PTEN 5874 0.078 0.44 NO
38 PRKACA PRKACA PRKACA 5883 0.078 0.45 NO
39 FGFR1OP2 FGFR1OP2 FGFR1OP2 6130 0.071 0.44 NO
40 PLCG1 PLCG1 PLCG1 6668 0.057 0.42 NO
41 PRKAR2A PRKAR2A PRKAR2A 6694 0.056 0.42 NO
42 MAPKAP1 MAPKAP1 MAPKAP1 6743 0.054 0.42 NO
43 CBL CBL CBL 6944 0.05 0.41 NO
44 SPRY2 SPRY2 SPRY2 7085 0.047 0.4 NO
45 CALM3 CALM3 CALM3 7092 0.047 0.41 NO
46 BAD BAD BAD 7494 0.04 0.39 NO
47 AKT2 AKT2 AKT2 7538 0.039 0.39 NO
48 STAT3 STAT3 STAT3 7573 0.038 0.39 NO
49 ADCY6 ADCY6 ADCY6 7627 0.037 0.39 NO
50 ADCY7 ADCY7 ADCY7 7678 0.036 0.39 NO
51 PRKAR1A PRKAR1A PRKAR1A 7769 0.035 0.38 NO
52 CALM1 CALM1 CALM1 7817 0.034 0.38 NO
53 CASP9 CASP9 CASP9 7954 0.032 0.38 NO
54 CREB1 CREB1 CREB1 8057 0.03 0.38 NO
55 SOS1 SOS1 SOS1 8071 0.029 0.38 NO
56 TSC2 TSC2 TSC2 8168 0.028 0.37 NO
57 UBA52 UBA52 UBA52 8251 0.027 0.37 NO
58 PDPK1 PDPK1 PDPK1 8498 0.022 0.36 NO
59 FRS3 FRS3 FRS3 8630 0.021 0.35 NO
60 PIK3CA PIK3CA PIK3CA 8702 0.02 0.35 NO
61 FOXO3 FOXO3 FOXO3 8799 0.018 0.35 NO
62 PRKACG PRKACG PRKACG 8877 0.017 0.34 NO
63 CUX1 CUX1 CUX1 8979 0.015 0.34 NO
64 GRB2 GRB2 GRB2 9073 0.014 0.33 NO
65 ADCY8 ADCY8 ADCY8 9078 0.014 0.34 NO
66 FRS2 FRS2 FRS2 9246 0.011 0.33 NO
67 PRKAR1B PRKAR1B PRKAR1B 9259 0.011 0.33 NO
68 MKNK1 MKNK1 MKNK1 9332 0.0098 0.32 NO
69 STAT1 STAT1 STAT1 9407 0.0085 0.32 NO
70 RPS27A RPS27A RPS27A 9528 0.0069 0.31 NO
71 CALM2 CALM2 CALM2 9674 0.0049 0.31 NO
72 THEM4 THEM4 THEM4 9736 0.004 0.3 NO
73 BRAF BRAF BRAF 9777 0.0036 0.3 NO
74 MDM2 MDM2 MDM2 9919 0.0014 0.29 NO
75 FGF23 FGF23 FGF23 9988 0.00061 0.29 NO
76 RAF1 RAF1 RAF1 10029 0.0001 0.29 NO
77 AKT1S1 AKT1S1 AKT1S1 10089 -0.00061 0.28 NO
78 FGF22 FGF22 FGF22 10110 -0.00082 0.28 NO
79 MAPK3 MAPK3 MAPK3 10227 -0.0026 0.28 NO
80 RICTOR RICTOR RICTOR 10240 -0.0028 0.28 NO
81 PPP2CB PPP2CB PPP2CB 10303 -0.0037 0.27 NO
82 ADCY3 ADCY3 ADCY3 10333 -0.0041 0.27 NO
83 MAPK1 MAPK1 MAPK1 10363 -0.0046 0.27 NO
84 MLST8 MLST8 MLST8 10365 -0.0046 0.27 NO
85 AKT1 AKT1 AKT1 10625 -0.0084 0.26 NO
86 PPP2R1A PPP2R1A PPP2R1A 10647 -0.0088 0.26 NO
87 SHC1 SHC1 SHC1 10732 -0.01 0.25 NO
88 GSK3A GSK3A GSK3A 10942 -0.013 0.24 NO
89 FGFR4 FGFR4 FGFR4 11417 -0.019 0.22 NO
90 MAP2K2 MAP2K2 MAP2K2 11498 -0.02 0.22 NO
91 KLB KLB KLB 11719 -0.022 0.21 NO
92 YWHAB YWHAB YWHAB 12084 -0.027 0.19 NO
93 TRIM24 TRIM24 TRIM24 12103 -0.027 0.19 NO
94 MTOR MTOR MTOR 12188 -0.028 0.19 NO
95 ADRBK1 ADRBK1 ADRBK1 12436 -0.032 0.17 NO
96 PPP2CA PPP2CA PPP2CA 12740 -0.036 0.16 NO
97 KRAS KRAS KRAS 12775 -0.037 0.16 NO
98 FGF8 FGF8 FGF8 12804 -0.037 0.16 NO
99 MAP2K1 MAP2K1 MAP2K1 13417 -0.045 0.13 NO
100 ZMYM2 ZMYM2 ZMYM2 13594 -0.048 0.12 NO
101 CHUK CHUK CHUK 13617 -0.048 0.13 NO
102 CDKN1A CDKN1A CDKN1A 13711 -0.049 0.12 NO
103 CPSF6 CPSF6 CPSF6 13777 -0.05 0.12 NO
104 PRKCD PRKCD PRKCD 13877 -0.052 0.12 NO
105 BCR BCR BCR 13916 -0.052 0.12 NO
106 SRC SRC SRC 13949 -0.053 0.12 NO
107 MYO18A MYO18A MYO18A 14063 -0.055 0.12 NO
108 NRAS NRAS NRAS 15221 -0.077 0.064 NO
109 FGF17 FGF17 FGF17 15378 -0.08 0.06 NO
110 RPS6KB2 RPS6KB2 RPS6KB2 15386 -0.08 0.065 NO
111 FGF3 FGF3 FGF3 15537 -0.084 0.062 NO
112 PHLPP1 PHLPP1 PHLPP1 16059 -0.098 0.04 NO
113 FGF4 FGF4 FGF4 16634 -0.12 0.016 NO
114 HRAS HRAS HRAS 16731 -0.12 0.019 NO
115 FGFR1OP FGFR1OP FGFR1OP 16981 -0.14 0.014 NO
116 ITPR3 ITPR3 ITPR3 17147 -0.15 0.014 NO
117 FGF19 FGF19 FGF19 17484 -0.17 0.0064 NO
118 CDK1 CDK1 CDK1 18021 -0.24 -0.0081 NO
119 TRIB3 TRIB3 TRIB3 18330 -0.29 -0.0069 NO
120 FGFR3 FGFR3 FGFR3 18676 -0.46 0.0026 NO

Figure S57.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table S30.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GNAO1 GNAO1 GNAO1 34 0.9 0.16 YES
2 GLI1 GLI1 GLI1 562 0.57 0.24 YES
3 GNAZ GNAZ GNAZ 1406 0.42 0.26 YES
4 GNG2 GNG2 GNG2 1680 0.38 0.32 YES
5 GLI3 GLI3 GLI3 1829 0.35 0.37 YES
6 RAB23 RAB23 RAB23 1903 0.34 0.43 YES
7 GLI2 GLI2 GLI2 2337 0.3 0.46 YES
8 PTCH1 PTCH1 PTCH1 2769 0.25 0.49 YES
9 SMO SMO SMO 2851 0.24 0.53 YES
10 GNAI2 GNAI2 GNAI2 4749 0.12 0.45 NO
11 SPOP SPOP SPOP 4793 0.12 0.46 NO
12 SUFU SUFU SUFU 5122 0.1 0.47 NO
13 SAP30 SAP30 SAP30 5301 0.098 0.48 NO
14 GNAI1 GNAI1 GNAI1 5463 0.092 0.48 NO
15 ARRB2 ARRB2 ARRB2 5534 0.09 0.5 NO
16 PRKACA PRKACA PRKACA 5883 0.078 0.49 NO
17 SSPO SSPO SSPO 6305 0.066 0.48 NO
18 FOXA2 FOXA2 FOXA2 6555 0.06 0.48 NO
19 CREBBP CREBBP CREBBP 6771 0.054 0.48 NO
20 FBXW11 FBXW11 FBXW11 7097 0.047 0.47 NO
21 PIAS1 PIAS1 PIAS1 7684 0.036 0.44 NO
22 SIN3B SIN3B SIN3B 7722 0.036 0.45 NO
23 KIF3A KIF3A KIF3A 8668 0.02 0.4 NO
24 SHH SHH SHH 8810 0.018 0.4 NO
25 IFT172 IFT172 IFT172 9164 0.012 0.38 NO
26 CSNK1G3 CSNK1G3 CSNK1G3 9234 0.011 0.38 NO
27 GNB1 GNB1 GNB1 9380 0.0089 0.37 NO
28 CSNK1D CSNK1D CSNK1D 9816 0.0031 0.35 NO
29 RBBP4 RBBP4 RBBP4 9946 0.0011 0.34 NO
30 SAP18 SAP18 SAP18 9973 0.00082 0.34 NO
31 SIN3A SIN3A SIN3A 10010 0.00031 0.34 NO
32 CSNK1E CSNK1E CSNK1E 10282 -0.0033 0.32 NO
33 RBBP7 RBBP7 RBBP7 10533 -0.0071 0.31 NO
34 AKT1 AKT1 AKT1 10625 -0.0084 0.31 NO
35 CSNK1G2 CSNK1G2 CSNK1G2 11228 -0.017 0.28 NO
36 MTSS1 MTSS1 MTSS1 11566 -0.021 0.26 NO
37 IFT88 IFT88 IFT88 12452 -0.032 0.22 NO
38 CSNK1A1 CSNK1A1 CSNK1A1 12780 -0.037 0.21 NO
39 MAP2K1 MAP2K1 MAP2K1 13417 -0.045 0.19 NO
40 GNAI3 GNAI3 GNAI3 13695 -0.049 0.18 NO
41 STK36 STK36 STK36 13773 -0.05 0.19 NO
42 GSK3B GSK3B GSK3B 13858 -0.052 0.19 NO
43 PRKCD PRKCD PRKCD 13877 -0.052 0.2 NO
44 HDAC1 HDAC1 HDAC1 14330 -0.06 0.19 NO
45 CSNK1G1 CSNK1G1 CSNK1G1 14439 -0.061 0.19 NO
46 LGALS3 LGALS3 LGALS3 14717 -0.066 0.19 NO
47 HDAC2 HDAC2 HDAC2 14742 -0.067 0.2 NO
48 XPO1 XPO1 XPO1 15370 -0.08 0.18 NO

Figure S59.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Methods & Data
Input

  • Gene set database = c2.cp.v4.0.symbols.gmt

  • Expression data file = STES-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = STES-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)
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